[{"hash":"2086091616926776317","title":"Cortical neuron migration and signaling","description":"This cluster centers on neuronal development and cell movement, with notable GO terms for cortical radially oriented neuron migration, GABAergic interneuron development, and regulation of Rho-mediated signaling, pointing to cytoskeletal rearrangements and neural migration. While a couple of terms (bone resorption, light detection) are less connected, the dominant pattern supports neural development and migration signaling.","confidence":"Medium","size":29,"edges":302,"triangles":1920,"max_degree":26,"top_function":"protein localization to plasma membrane","top_go_terms":[{"id":"GO:0045453","count":13},{"id":"GO:0006813","count":13},{"id":"GO:0000160","count":13},{"id":"GO:0018298","count":13},{"id":"GO:0009584","count":13}]},{"hash":"2121622050829342096","title":"Aminoacyl-tRNA synthetases and translation","description":"The top GO terms are dominated by multiple aminoacyl-tRNA synthetases (isoleucyl-, methionyl-, valyl-, leucyl-) and translation, including regulation of translational fidelity, indicating a cluster centered on tRNA charging and protein synthesis. Some additional terms seem incidental noise rather than defining features. This suggests the core function is translation machinery.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0006428","count":6},{"id":"GO:0006431","count":6},{"id":"GO:0006438","count":6},{"id":"GO:0006450","count":6},{"id":"GO:0006412","count":6}]},{"hash":"2046965774138764443","title":"Cell Cycle and RNA Modification Cofactor Biosynthesis","description":"This cluster centers on cell cycle regulation and DNA-templated transcription, with additional enrichment for tRNA wobble uridine thiolation and biosynthesis of cofactors (thiamine and molybdenum cofactor). The mix suggests a broad, housekeeping regulatory program linking growth and RNA processing with essential metabolic pathways, though some annotations (e.g., neddylation, defense response) may reflect cross-talk or annotation noise.","confidence":"Medium","size":29,"edges":13,"triangles":0,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051726","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0002143","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0006777","count":2}]},{"hash":"1112887432199539052","title":"ER stress\u2013linked ubiquitin signaling and autophagy","description":"This cluster is driven by GO terms connecting ER-associated degradation (ERAD), ubiquitin-related processes (free ubiquitin chains, deubiquitination), and autophagosome maturation, plus ER-stress\u2013responsive apoptotic signaling. Together these suggest a common theme of cellular protein quality control under stress, with several outliers (DNA repair, spindle pole body duplication, NK cell regulation) that may reflect broader or adjacent functions in the same protein set. Overall, the dominant pattern supports a role in ER stress\u2013related proteostasis and autophagy regulation.","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1904378","count":1},{"id":"GO:1901340","count":1},{"id":"GO:0030474","count":1},{"id":"GO:1903094","count":1},{"id":"GO:0006289","count":1}]},{"hash":"1379750549004787402","title":"Bacterial Biosynthesis and Gene Expression","description":"The cluster's top GO terms cluster around biosynthetic pathways (cobalamin, antibiotic, lipid A) and cell wall organization, together with core expression machinery (translation, transcription) and regulation (negative regulation of translation, response to antibiotic). This pattern suggests a prokaryotic module integrating metabolism with protein synthesis and cell envelope assembly, rather than a single narrow process.","confidence":"Medium","size":29,"edges":315,"triangles":2289,"max_degree":27,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0006461","count":2},{"id":"GO:0046677","count":2}]},{"hash":"743507849527414857","title":"Chromatin methylation and transcriptional regulation","description":"This cluster centers on chromatin-related processes: rDNA heterochromatin formation, rRNA methylation, and DNA-templated transcription, along with multiple protein/peptide methylation events. These themes point to epigenetic control of gene expression as the core function, with additional signals for proteostasis (mitophagy and ubiquitin-mediated transport) suggesting broader cellular quality control involvement.","confidence":"Medium","size":29,"edges":393,"triangles":3331,"max_degree":28,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000183","count":13},{"id":"GO:0031167","count":9},{"id":"GO:0006351","count":8},{"id":"GO:0000117","count":7},{"id":"GO:0018027","count":7}]},{"hash":"42473378585704957","title":"Transcriptional Regulation & Oxidative/ER Stress","description":"The cluster shows enrichment for DNA-templated transcription and regulation of transcription by RNA polymerase II, along with ER stress response and redox homeostasis. This pattern points to regulatory proteins whose primary function is gene expression control and managing cellular stress (oxidative and ER). While there are some outliers like nervous system development and B cell signaling, the dominant terms suggest a cohesive theme around transcriptional regulation tied to stress response.","confidence":"Medium","size":29,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":8},{"id":"GO:0046826","count":7},{"id":"GO:0055114","count":6},{"id":"GO:0098869","count":5},{"id":"GO:0045454","count":5}]},{"hash":"1585975143307904853","title":"Rho/Rac signaling\u2013driven actin remodeling and cell migration","description":"Proteins here are dominated by terms related to Rho and Rac signaling, actin cytoskeleton organization, and the assembly of filopodia and lamellipodia, all key for actin-driven cell migration. While heart development and some signaling terms appear, the core theme is cytoskeletal dynamics governed by Rho/Rac pathways, supporting motility and morphological changes.","confidence":"High","size":29,"edges":65,"triangles":15,"max_degree":13,"top_function":"microtubule-based movement","top_go_terms":[{"id":"GO:0035023","count":6},{"id":"GO:0007507","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0030036","count":5},{"id":"GO:0098761","count":5}]},{"hash":"1754769822296660830","title":"Mitochondrial Electron Transport and Redox Metabolism","description":"This cluster shows terms linked to mitochondrial respiration (mitochondrial electron transport, cytochrome c to oxygen, cytochrome c\u2011heme linkage) and proton transmembrane transport, indicating components of oxidative phosphorylation. Additional terms like ethanol oxidation and retinol metabolic processes suggest broader redox-associated metabolism, but the strongest signal is mitochondrial energy production.","confidence":"High","size":29,"edges":50,"triangles":2,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006069","count":2},{"id":"GO:0006068","count":2},{"id":"GO:0042572","count":2},{"id":"GO:0017196","count":2}]},{"hash":"1999283333030927224","title":"GPCR signaling with innate immune response","description":"The set is enriched for GPCR-mediated signaling terms (adenylate cyclase activation, PLC-activating GPCR signaling) and the Toll-like receptor 8 pathway with defense against virus, plus several hormonal/neural processes (acetylcholine metabolism, thyroid-stimulating hormone signaling) and regulatory processes like axonogenesis and osteoclast differentiation. This points to a cluster of signaling pathways spanning immune, neural, and endocrine systems rather than a single precise function.","confidence":"Medium","size":29,"edges":59,"triangles":6,"max_degree":9,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034158","count":25},{"id":"GO:0060408","count":25},{"id":"GO:0007190","count":25},{"id":"GO:0007200","count":25},{"id":"GO:0009992","count":25}]},{"hash":"259638581207082546","title":"Neuronal development and microtubule dynamics","description":"The terms converge on cytoplasmic microtubule organization, nucleation, and spindle-related processes, along with neuron differentiation and migration, and mechanosensory signaling. This suggests a cluster of proteins involved in neuronal cytoskeleton mechanics and neurodevelopment. Some spindle-related terms reflect general cytoskeletal machinery, but the neuronal development and mechanosensory themes dominate.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031122","count":1},{"id":"GO:0030182","count":1},{"id":"GO:1903087","count":1},{"id":"GO:0071353","count":1},{"id":"GO:1905792","count":1}]},{"hash":"574084425505730658","title":"Splicing Regulation and RNA Silencing","description":"The cluster is enriched for mRNA splicing (via spliceosome), regulation and alternative splicing, mRNA modification, and RNA silencing pathways (ncRNA/miRNA-mediated), indicating a cohesive set of proteins involved in post-transcriptional RNA processing and gene regulation.","confidence":"High","size":29,"edges":237,"triangles":1390,"max_degree":24,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0048026","count":12},{"id":"GO:0010610","count":12},{"id":"GO:0031047","count":11},{"id":"GO:0006378","count":10},{"id":"GO:1901407","count":9}]},{"hash":"1171151574337749177","title":"Unknown","description":"The Top Terms span apoptosis, cell cycle regulation, differentiation, circadian gene expression, and diverse metabolic processes, with no single shared function and no observed interactions among members, making it impossible to assign a coherent, specific label to this cluster.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000210","count":1},{"id":"GO:0071158","count":1},{"id":"GO:0072332","count":1},{"id":"GO:0009303","count":1},{"id":"GO:0001649","count":1}]},{"hash":"1562273055681504554","title":"RNA processing and translational control","description":"This cluster is enriched for terms tied to post-transcriptional regulation: translation initiation and reinitiation, splicing regulation, ncRNA- and miRNA-mediated silencing, and mRNA modification, suggesting a cohesive theme of RNA processing and control of gene expression at the translational level (with some developmental context).","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":6},{"id":"GO:0002188","count":6},{"id":"GO:0000381","count":5},{"id":"GO:0031047","count":5},{"id":"GO:0006378","count":5}]},{"hash":"1585178290566590522","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000380","count":1},{"id":"GO:0030422","count":1},{"id":"GO:0051209","count":1},{"id":"GO:0010087","count":1},{"id":"GO:0048024","count":1}]},{"hash":"942372664571787783","title":"Unknown","description":"The top GO terms cover a mix of cytoskeletal dynamics (lamellipodium morphogenesis, dendritic spine maintenance), immune/hematopoietic processes (myeloid homeostasis, progenitor proliferation, neutrophil apoptosis regulation), plant-specific pollen guidance, and metabolic/lipid biosynthesis, with no coherent single theme tying all proteins together. Therefore there isn\u2019t a clear, representative label for this cluster.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1905524","count":2},{"id":"GO:2000394","count":2},{"id":"GO:0097062","count":1},{"id":"GO:0002262","count":1},{"id":"GO:0033030","count":1}]},{"hash":"623837450025726477","title":"Ribosome biogenesis and rRNA processing","description":"This cluster is driven by GO terms centered on assembling and maturing the large ribosomal subunit and processing rRNA (large subunit assembly, LSU-rRNA maturation, preribosome assembly, snoRNA release from pre-rRNA), indicating a coherent theme in ribosome biogenesis; other terms like virus defense or metabolism appear incidental.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0000463","count":1},{"id":"GO:1902626","count":1},{"id":"GO:0010501","count":1}]},{"hash":"1656329524974940144","title":"DNA replication/repair and transcription","description":"The top GO terms are concentrated on nucleic acid processes\u2014DNA duplex unwinding, error-prone translesion synthesis, DNA-templated transcription, and nonsense-mediated decay\u2014suggesting a core theme of DNA metabolism and RNA processing. A few terms relate to proteoglycan biosynthesis and Golgi-to-plasma membrane transport, which may reflect broader cellular roles but do not define a single cohesive alternative theme. Overall, the cluster seems to group proteins involved in DNA damage tolerance and gene expression.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032508","count":3},{"id":"GO:0042276","count":2},{"id":"GO:0030210","count":2},{"id":"GO:0015012","count":2},{"id":"GO:0000184","count":2}]},{"hash":"2026023529560330897","title":"Mycobacterial capsule and cell wall biosynthesis","description":"The cluster is dominated by GO terms for capsule polysaccharide biosynthesis, mycolate cell wall layer assembly, and cell wall polysaccharide biosynthesis, with UDP-D-galactose metabolic process supporting wall/capsule component production. While some transport terms are present, the strongest signal ties to cell envelope construction typical of mycobacteria, justifying a label focused on capsule and cell wall biosynthesis.","confidence":"High","size":29,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045227","count":2},{"id":"GO:0071769","count":2},{"id":"GO:0070592","count":2},{"id":"GO:0052573","count":2},{"id":"GO:1901481","count":1}]},{"hash":"2157739676146062809","title":"Photosynthesis Light-Response Proteins","description":"The cluster is dominated by GO terms tied to photosynthesis and light responses (photosynthesis, light harvesting in PSII, nonphotochemical quenching, responses to blue/red/UV-A light, and high/low light). This points to proteins involved in light capture, energy transfer, and photoprotective regulation in photosynthetic systems, with related chlorophyll/chromophore associations. Thus a label focusing on light-driven photosynthesis best represents the shared function.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0015979","count":5},{"id":"GO:0071486","count":4},{"id":"GO:0009645","count":4},{"id":"GO:0018298","count":4},{"id":"GO:1904964","count":4}]},{"hash":"220247904005255152","title":"Unknown","description":"Unknown","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0001081","count":2},{"id":"GO:1902138","count":2},{"id":"GO:0009718","count":2}]},{"hash":"571011446815408434","title":"Signaling, ubiquitination, and cytoskeleton regulation","description":"The GO terms indicate roles in ubiquitin-proteasome proteolysis, regulation of GTPase activity, actin nucleation via Arp2/3, and modulation of tyrosine kinase signaling, with hints of development (forebrain and skeletal morphogenesis). This spread suggests a functional cluster centered on coordinated signaling control, proteostasis, and cytoskeletal dynamics rather than a single pathway.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0048705","count":2},{"id":"GO:0070317","count":2},{"id":"GO:0030900","count":2}]},{"hash":"2076253491990418467","title":"Unknown","description":"The Top Terms are highly diverse, spanning inflammatory response, axonogenesis, kinase regulation, plant-specific processes (gibberellin response, trichome patterning), DNA repair, viral processes, and transcription/telomere localization. There is no single coherent function or pathway tying these terms together, suggesting the cluster represents a heterogeneous mix rather than a shared biological role.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006954","count":3},{"id":"GO:0007409","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0009739","count":2},{"id":"GO:1900033","count":2}]},{"hash":"1618146571013738044","title":"GPCR Signaling and Innate Immunity","description":"The cluster centers on G protein-coupled receptor signaling (adenylate cyclase activation, PLC-mediated pathways) and innate immune responses (TLR8 signaling, defense against virus). Additional terms reflect neural/endocrine signaling within broader signaling networks, supporting a cohesive theme around signal transduction with immune components.","confidence":"Medium","size":29,"edges":284,"triangles":1607,"max_degree":26,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034158","count":27},{"id":"GO:0060408","count":27},{"id":"GO:0007190","count":27},{"id":"GO:0007200","count":27},{"id":"GO:0009992","count":27}]},{"hash":"1931102116077018618","title":"Mitochondrial Transport and Membrane Potential","description":"The terms cluster around mitochondrial inner membrane transport (ADP/ATP, alpha-ketoglutarate) and regulation of membrane permeability and membrane potential, with magnesium export supporting energy metabolism. While insulin/ IGF signaling terms appear, the dominant theme is mitochondrial transport and energetic regulation.","confidence":"High","size":29,"edges":4,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0097274","count":14},{"id":"GO:0070542","count":12},{"id":"GO:0046902","count":11},{"id":"GO:0051881","count":11},{"id":"GO:0015742","count":11}]},{"hash":"776546428609850515","title":"Interferon-mediated antiviral innate response","description":"The top GO terms point to innate immunity with strong signals for cellular response to type I interferon, dsRNA recognition, and antiviral defense, suggesting a theme around interferon-driven antiviral innate immunity. Some terms (e.g., plant hormone signaling and GPCR regulation) appear less related and may reflect annotation overlap or broader functional diversity, but the dominant pattern supports an interferon/innate antiviral focus.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0051301","count":6},{"id":"GO:0071357","count":6},{"id":"GO:0009938","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0045087","count":4}]},{"hash":"995415204257190551","title":"Innate immune sensing and inflammasome activation","description":"The GO terms emphasize cellular response to lipopolysaccharide, Toll-like receptor signaling, and NLRP3 inflammasome complex assembly, indicating a cluster enriched for innate immune detection and inflammatory signaling. While some terms are obsolete or less directly related (e.g., xenobiotic transport), the core theme centers on host-pathogen recognition and inflammasome-driven responses.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071222","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0006855","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0055114","count":1}]},{"hash":"941374390784220177","title":"NF-kappaB\u2013Mediated Inflammation and Chemokine Production","description":"This cluster centers on inflammatory signaling and chemokine production, including NF-kappaB regulation, chemokine (e.g., CCL5/MIP-1\u03b1) production, and cell migration, with some vesicle trafficking terms tied to mediator secretion. Collectively, these terms point to an immune/inflammatory response module rather than a single structural or metabolic function. ","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035544","count":3},{"id":"GO:0086070","count":2},{"id":"GO:1903444","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0007253","count":2}]},{"hash":"359304506587120503","title":"Endocytic trafficking and MVB sorting","description":"The top GO terms cluster around vesicle transport and sorting in the endomembrane system, including ER-to-Golgi and Golgi-to-ER transport, endosome-to-melanosome transport, endocytic recycling, and multivesicular body (MVB) assembly and sorting. These collectively point to a set of proteins involved in vesicle formation, trafficking, and MVB biogenesis. A few terms (like bone resorption or beta selection) seem less related and may reflect annotation noise, but the core theme is vesicular trafficking and MVB pathways.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006890","count":4},{"id":"GO:0035646","count":4},{"id":"GO:0032456","count":4},{"id":"GO:0010458","count":4},{"id":"GO:0045453","count":4}]},{"hash":"1901878001416502749","title":"Vertebrate Development and Stress Signaling","description":"This cluster's top GO terms point to tissue development (skin, skeletal morphogenesis, multicellular organism development) alongside stress-related and proteostasis pathways (ER-stress\u2013induced apoptosis, ubiquitin-proteasome degradation, poly-ADP-ribosylation) and regulatory processes affecting cell cycle and cardiac electrical activity (G0 to G1 transition, SA node action potential). The combination suggests proteins that participate in development and tissue maintenance while integrating stress responses and protein homeostasis. Confidence: Medium","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0051260","count":6},{"id":"GO:0070059","count":6},{"id":"GO:0043588","count":6},{"id":"GO:0007275","count":6},{"id":"GO:0035994","count":6}]},{"hash":"1055608216075214665","title":"Unknown","description":"The set of terms spans telomere protection/heterochromatin, DNA structure (G-quadruplex), plant hormone signaling, and several animal development and metabolism terms with little overlap, and there are no protein\u2013protein edges connecting them. Because there isn't a unifying function across these terms, a stable label cannot be assigned beyond Unknown.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0031848","count":4},{"id":"GO:0071919","count":4},{"id":"GO:0035390","count":4},{"id":"GO:0021983","count":4}]},{"hash":"1769976157384837242","title":"Aromatic compound catabolism and detoxification","description":"The Top Terms include beta-ketoadipate pathway, 3-phenylpropionate catabolic process, phosphatidylserine catabolic process, cellular oxidant detoxification, and the epoxygenase P450 pathway, all pointing to metabolism and breakdown of aromatic/xenobiotic compounds and detoxification; a few terms like secondary shoot formation may reflect broader annotation, but the core theme remains aromatic compound degradation and detoxification.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":14},{"id":"GO:0019373","count":11},{"id":"GO:0010223","count":11},{"id":"GO:0055114","count":11},{"id":"GO:0098869","count":11}]},{"hash":"198251571361952507","title":"ESCRT- and ERAD-Linked Protein Quality Control","description":"The cluster centers on ubiquitin-mediated degradation and membrane trafficking: ESCRT-dependent viral budding, ER-to-cytosol transport (ERAD), and regulation of protein localization, with some peripheral terms like nuclear localization or cell death. This points to a theme of intracellular protein quality control and turnover, though a few terms are less directly related.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0039702","count":2},{"id":"GO:0031134","count":1},{"id":"GO:1903094","count":1},{"id":"GO:0030970","count":1},{"id":"GO:0061060","count":1}]},{"hash":"1345483743925525672","title":"Ribosome Biogenesis and RNA Processing","description":"The dominant GO terms point to rRNA maturation (SSU/LSU, 5.8S), ribosomal subunit biogenesis, and RNA processing (including mRNA splicing) within the nucleus, with additional signals for transcription regulation and chromatin remodeling. Together, these indicate a core role in RNA metabolism and ribosome assembly. Thus, this label best captures the common function of the cluster.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":3},{"id":"GO:0000462","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0000398","count":2}]},{"hash":"1102695635160753738","title":"Proteoglycan (ECM) Biosynthesis and Development","description":"This cluster is dominated by GO terms for heparan sulfate and heparin proteoglycan biosynthesis, and includes an endomembrane system organization term, which together suggest a core function in producing extracellular matrix components (glycosaminoglycans/proteoglycans) that participate in signaling during development. The presence of BMP signaling and embryonic development terms supports a developmental role for these ECM/biosynthetic proteins, while some plant polysaccharide biosynthesis terms reflect broader glycan biosynthesis processes across species. Overall, the common theme is proteoglycan/ECM biosynthesis linked to developmental signaling.","confidence":"Medium","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030210","count":1},{"id":"GO:0010417","count":1},{"id":"GO:0015012","count":1},{"id":"GO:0072498","count":1},{"id":"GO:0015014","count":1}]},{"hash":"1079235192712347819","title":"Unknown","description":"The cluster's top GO terms are highly heterogeneous, covering immune signaling (interleukin-4/IL-15 pathways and lymphocyte proliferation), metabolism (GMP/GTP biosynthesis, purine metabolism), development (retina development), and interactions with fungi, with no clear shared function among the proteins and no observed edges linking them. Therefore no coherent label can be assigned.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071353","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0046651","count":1},{"id":"GO:0006177","count":1},{"id":"GO:0006183","count":1}]},{"hash":"2057768132902652810","title":"Unknown","description":"The GO terms cover neural development, immune/defense responses, metal ion and ER-stress signaling, RNA transport, cell cycle, dephosphorylation, TORC1 signaling, and imprinting regulation, which are disparate functions with no single clear theme linking all 29 proteins. This makes a concise, representative label unreliable.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0071276","count":2},{"id":"GO:0051028","count":2}]},{"hash":"2056197068020839014","title":"Ubiquitin-Mediated Regulation of Apoptosis and Immune Signaling","description":"This cluster centers on ubiquitin-dependent regulation of cell fate and immune pathways. The top GO terms include protein polyubiquitination, negative regulation of apoptotic and necroptotic processes, regulation of Toll-like receptor signaling, and transcriptional regulation, all suggesting a cohesive role in modulating apoptosis, necroptosis, and innate immune responses through ubiquitin signaling. The mix of signaling and transcriptional control indicates a broader regulatory module rather than a single pathway, supporting a unified theme around stress-responsive regulation via ubiquitination.","confidence":"High","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":6},{"id":"GO:0043066","count":5},{"id":"GO:0034121","count":5},{"id":"GO:0000122","count":5},{"id":"GO:0060544","count":5}]},{"hash":"1108811750730536786","title":"Unknown","description":"This cluster shows a mix of GO terms spanning transcription regulation, immune signaling, spermatogenesis, and plant cell wall biosynthesis, with no single unifying function. The presence of xylan/xyloglucan metabolism alongside transcription-related terms and viral processes suggests disparate annotations rather than a coherent cluster function.","confidence":"","size":29,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0042345","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0007283","count":2},{"id":"GO:0006351","count":2}]},{"hash":"491244686454611666","title":"Ribosome Biogenesis and Translation","description":"The strongest signals in the cluster are translation (GO:0006412) and ribosome biogenesis (GO:0042254), suggesting these proteins are tied to protein synthesis and ribosome assembly. The presence of an antibiotic response term supports a link to ribosome-targeted processes. Other terms like vacuolar acidification and calcium signaling appear secondary but do not negate the core translation/ribosome theme. Overall, the cluster is best described by ribosome biogenesis and translation functions.","confidence":"High","size":28,"edges":106,"triangles":297,"max_degree":15,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":9},{"id":"GO:0046677","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0007035","count":3},{"id":"GO:0042994","count":3}]},{"hash":"371914691797302057","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":171,"triangles":658,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006541","count":9},{"id":"GO:0001889","count":6},{"id":"GO:0042594","count":6},{"id":"GO:0006207","count":6},{"id":"GO:0044205","count":6}]},{"hash":"2002562903485504285","title":"Ubiquitination and ERAD-driven protein quality control","description":"This cluster is dominated by GO terms for ubiquitination (autoubiquitination, ubiquitin-dependent ERAD, and K63-linked ubiquitination), indicating a focus on tagging proteins for degradation and proteostasis. Additional terms point to stress- and hormone-related regulation of protein homeostasis and chaperone-mediated assembly, consistent with a network coordinating protein quality control under cellular stress.","confidence":"High","size":28,"edges":80,"triangles":36,"max_degree":18,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":20},{"id":"GO:0030433","count":18},{"id":"GO:0070534","count":17},{"id":"GO:0090035","count":13},{"id":"GO:0071361","count":13}]},{"hash":"980501404731346360","title":"Endomembrane trafficking and ESCRT-mediated processes","description":"The top GO terms center on vesicle trafficking and ESCRT machinery: Golgi retention, vacuole fusion, MVB sorting, exosomal secretion, and ESCRT-driven viral budding. These points strongly suggest a cohesive role in endomembrane trafficking and vesicle formation/secretion, with related cell division processes like septum digestion and mitotic chromosome condensation reflecting membrane remodeling during cytokinesis. ","confidence":"High","size":28,"edges":22,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0030447","count":4},{"id":"GO:0045053","count":4},{"id":"GO:0042144","count":3},{"id":"GO:0071454","count":3},{"id":"GO:0090611","count":3}]},{"hash":"1937532477973042736","title":"Ubiquitin-Proteasome\u2013Mediated Protein Degradation","description":"The top GO terms revolve around ubiquitination and proteasomal degradation (ubiquitin-dependent catabolic processes, polyubiquitination, SCF-dependent proteasomal degradation, ERAD pathway), signaling a cohesive group of proteins involved in tagging substrates for destruction. A few terms touch on broader signaling (vitamin D response, I-kappaB phosphorylation), but the dominant theme is protein turnover via ubiquitination. Confidence: High","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":12},{"id":"GO:0000209","count":10},{"id":"GO:0051865","count":8},{"id":"GO:0031146","count":8},{"id":"GO:0030433","count":7}]},{"hash":"307541479155506009","title":"Innate immune signaling and xenophagy","description":"Top terms point to defense against bacteria, LPS signaling, interferon-beta production, and positive regulation of xenophagy, indicating innate immune signaling and autophagic pathogen handling; other terms reflect broader stress or regulatory processes, making them less defining for the cluster.","confidence":"Medium","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":2},{"id":"GO:0032436","count":2},{"id":"GO:0046690","count":2},{"id":"GO:0043433","count":2},{"id":"GO:1904417","count":2}]},{"hash":"1322430285597129617","title":"RNAP II Transcription Initiation Regulators","description":"These proteins show GO terms centered on RNA polymerase II transcription initiation and preinitiation complex assembly (e.g., RNA polymerase II preinitiation complex assembly; transcription initiation at RNA polymerase II promoter), which suggests a shared role in initiating and regulating transcription. Additional terms indicate regulatory activities (negative regulation of protein kinase activity; positive regulation of post-transcriptional gene silencing) and more distant connections to vesicle trafficking and viral processes, implying possible multifunctionality or annotation noise. Overall, the strongest cohesive signal is transcription initiation/regulation, supporting a label of transcription initiation regulators with a broad regulatory scope.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0043923","count":1},{"id":"GO:0051123","count":1},{"id":"GO:0006367","count":1},{"id":"GO:1900370","count":1}]},{"hash":"57558650315776062","title":"Mitochondrial import and mitophagy","description":"The cluster's top GO terms center on mitochondrial processes\u2014mitophagy and import of proteins into the mitochondrial matrix\u2014indicating participation in mitochondrial maintenance and protein trafficking. A few SRP-associated membrane targeting terms are present but likely secondary, so the dominant theme is mitochondrial quality control via import and autophagy.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000422","count":2},{"id":"GO:0030150","count":2},{"id":"GO:0006614","count":1},{"id":"GO:0006617","count":1},{"id":"GO:0006616","count":1}]},{"hash":"1464070058870317053","title":"Bacterial capsule and cell wall biosynthesis","description":"The cluster is enriched for capsule polysaccharide biosynthetic process, cell wall organization, and arabinan biosynthesis, pointing to envelope biogenesis and surface polysaccharide production as a shared function. Other terms like cell division and regulation of cell shape align with envelope remodeling during growth, while metabolic terms such as cobalamin and methanol metabolism reflect broader bacterial physiology present in the set. Overall, the common theme is bacterial surface polysaccharide and cell wall biosynthesis and maintenance.","confidence":"High","size":28,"edges":35,"triangles":4,"max_degree":9,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0046677","count":10},{"id":"GO:0009236","count":8},{"id":"GO:0035884","count":7},{"id":"GO:0071555","count":7},{"id":"GO:0045227","count":7}]},{"hash":"2180043348132995696","title":"Neurodevelopment and axon guidance with angiogenesis","description":"This cluster is dominated by neural development and axon guidance GO terms (facioacoustic ganglion development; branchiomotor neuron axon guidance; retinal ganglion cell axon guidance; gonadotrophin-releasing hormone neuronal migration to the hypothalamus; facial nerve structural organization) and vascular-related processes (angiogenesis involved in coronary vascular morphogenesis; endothelial cell chemotaxis). The convergence of neural patterning, axon pathfinding, and angiogenic/neurovascular cues suggests a neurodevelopmental/axon-guidance theme intertwined with vascular morphogenesis, though a few terms like transcription termination and endosome localization are less aligned. Overall, the terms coalesce around developmentally coordinated neural and vascular patterning, supporting a cohesive label.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":2},{"id":"GO:1903375","count":2},{"id":"GO:0060978","count":2},{"id":"GO:0021828","count":2},{"id":"GO:1902336","count":2}]},{"hash":"1429377187426523217","title":"Telomere maintenance and stress-related transport","description":"This set highlights multiple transport processes (ascorbic and dehydroascorbic acids, trehalose, urate, organic anions) and stress responses (osmotic stress, insulin-stimulated glucose import), with GO terms linked to genome maintenance and telomere regulation (DNA recombination, telomere maintenance via telomerase, replicative senescence). The common thread is cellular stress and metabolic adaptation that intersects genome stability pathways, justifying a label around telomere maintenance alongside transport.","confidence":"Medium","size":28,"edges":12,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0019852","count":3},{"id":"GO:0006310","count":2},{"id":"GO:0032212","count":2},{"id":"GO:1904728","count":2},{"id":"GO:0044381","count":2}]},{"hash":"1384288323828699858","title":"Nucleocytoplasmic transport and transcription regulation","description":"The top GO terms cluster around nuclear import/export (NLS-bearing protein import into nucleus; ribosomal protein import into nucleus; positive regulation of protein export from nucleus) and DNA-templated transcription, indicating a core role in nucleocytoplasmic transport with linked transcriptional control. Additional signals for small GTPase signaling and intraflagellar transport suggest broader trafficking and regulatory connections.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006607","count":6},{"id":"GO:0043547","count":5},{"id":"GO:0046827","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0006610","count":4}]},{"hash":"95540670954736536","title":"Polysaccharide metabolism and storage","description":"The cluster shows strong representation of polysaccharide synthesis and degradation (glycogen, amylopectin/starch components, trehalose, sucrose) and related storage processes, indicating a core function in carbohydrate metabolism and storage. A minor note is the presence of poly-hydroxybutyrate biosynthesis terms, but the dominant theme remains polysaccharide metabolism.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042619","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0030980","count":1},{"id":"GO:0044245","count":1},{"id":"GO:0005978","count":1}]},{"hash":"2195820741659988165","title":"Developmental transcription and signaling regulators","description":"The terms cluster around developmental processes and regulation, including positive regulation of vasculogenesis, positive regulation of myoblast differentiation, and negative regulation of Notch signaling, plus DNA-templated transcription, suggesting proteins that modulate developmental signaling pathways and transcriptional programs. Some hydroxylation and biosynthetic terms appear as noise or annotation artifacts, but the dominant theme points to developmental gene regulation rather than metabolism or primary biosynthesis.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:2001214","count":6},{"id":"GO:0061428","count":6},{"id":"GO:0045746","count":6},{"id":"GO:0042264","count":6},{"id":"GO:0042265","count":6}]},{"hash":"607528005856648953","title":"Light-Responsive Photosynthesis Proteins","description":"The top GO terms cluster around photosynthesis-related processes and light responses (photosynthesis, light harvesting in PSII, nonphotochemical quenching, red light, UV-A, high/low light responses), suggesting these proteins participate in light capture, energy regulation, and photoprotection in chloroplasts. A single term about ER-Golgi transport appears incidental to the main theme. ","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0071486","count":2},{"id":"GO:0009645","count":2},{"id":"GO:0018298","count":2},{"id":"GO:1904964","count":2}]},{"hash":"530850019120719065","title":"Neuronal Excitability and Sensory Signaling","description":"The cluster is dominated by GO terms tied to membrane depolarization, ion transport (potassium and calcium), and excitatory postsynaptic potential, all indicative of neuronal signaling and synaptic activity. Additional terms point to sensory processing (sound perception) and reflexes, suggesting a cohesive theme around neural excitability and sensory processing; some outliers relate to broader signaling contexts but do not override the central neuronal pattern.","confidence":"High","size":28,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051899","count":3},{"id":"GO:0071805","count":3},{"id":"GO:0098703","count":3},{"id":"GO:0001988","count":2},{"id":"GO:2000344","count":2}]},{"hash":"1491501997710441571","title":"Developmental growth and stress response","description":"Top GO terms indicate a broad mix of developmental processes (mitotic cell cycle, multicellular organism development, stem cell proliferation, heart development, positive regulation of cell population proliferation) plus stress and nutrient signaling (SOS response, cellular response to hypoxia, response to nutrient) and other regulatory activities (visual perception, protein methylation). The overlap suggests a general theme of developmental growth coupled with stress-responsive regulation, rather than a single pathway, hence the label Developmental growth and stress response.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":4},{"id":"GO:0007275","count":3},{"id":"GO:0009432","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0072089","count":2}]},{"hash":"2099245726904168933","title":"ER stress and redox homeostasis","description":"This cluster is enriched for oxidative stress response and ER-related protein folding. Terms include cellular redox homeostasis, cellular oxidant detoxification, and protein folding in the endoplasmic reticulum, plus ER stress response, suggesting a common theme of managing redox balance and protein folding in the ER. Name reflects that.","confidence":"High","size":28,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0033158","count":1},{"id":"GO:0034599","count":1}]},{"hash":"1811950574413248377","title":"RNA Pseudouridylation and Translation","description":"The GO terms show strong enrichment for pseudouridine synthesis in tRNA, snRNA, and mRNA, plus translation, cytoplasmic translation, and translational initiation, pointing to a cluster of RNA modification enzymes closely tied to ribosome-mediated protein synthesis. A few other terms (antibiotic response, xenobiotic export, nucleotide-excision repair) are more peripheral and may reflect broader cellular stress, but do not define the main function of the cluster.","confidence":"High","size":28,"edges":10,"triangles":0,"max_degree":7,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0031119","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0031120","count":3},{"id":"GO:1990481","count":3}]},{"hash":"851983487602311261","title":"Transcriptional Regulation and Telomere Control","description":"The cluster is dominated by DNA-templated transcription and several telomere-related regulatory terms (telomere lengthening, telomere capping, telomere maintenance), with supporting hints from chromatin modification and development; additional Arp2/3/GTPase regulation and brain development terms suggest broader gene-regulatory and developmental roles that can accompany telomere and chromatin processes. The lack of interaction data (Edges 0) makes the grouping broad but coherent around transcriptional/chromatin control and genome stability.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007568","count":8},{"id":"GO:0043547","count":8},{"id":"GO:0007420","count":6},{"id":"GO:0051568","count":6},{"id":"GO:0034729","count":6}]},{"hash":"366192895129411293","title":"Neurotransmitter metabolism and endocrine response","description":"This cluster shows enrichment for dopamine catabolic process, regulation of serotonin secretion, and corticosterone response, combined with pituitary gland development, suggesting a coherent theme of neuroendocrine signaling and neurotransmitter regulation. Some terms are unrelated or obsolete, indicating mixed signals, but the core terms point to neurotransmitter metabolism and endocrine responsiveness. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0021983","count":9},{"id":"GO:0032496","count":9},{"id":"GO:0006355","count":7},{"id":"GO:0009228","count":7}]},{"hash":"529547716726678691","title":"Plant organellar RNA processing and editing","description":"The top GO terms cluster around chloroplast/plastid transcription, chloroplast RNA modification, plastid polycistronic mRNA processing, and mitochondrial RNA modification/editing, indicating RNA metabolism specific to plant organelles. Although there are seed development terms, the dominant theme ties to organellar RNA processing/editing in plants (chloroplasts and mitochondria). High","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007565","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0000961","count":2},{"id":"GO:0009793","count":2},{"id":"GO:0080156","count":2}]},{"hash":"2074445337101414908","title":"Heart and vascular morphogenesis","description":"This cluster shows strong representation of heart development and blood vessel morphogenesis terms (GO:0007507, GO:0001569), suggesting a group of proteins involved in cardiovascular tissue formation. The presence of cellular response to hypoxia and various kinase-related terms indicates signaling and regulatory processes that coordinate growth, shape changes, and autophosphorylation in cardiovascular contexts. Overall, the proteins appear linked to cardiovascular morphogenesis with some concurrent signaling roles.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001569","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0071456","count":3},{"id":"GO:0071902","count":3},{"id":"GO:0051028","count":3}]},{"hash":"2294327999525453855","title":"Lipid Metabolism and Detoxification","description":"The top GO terms are dominated by lipid-related processes (regulation of endocannabinoid signaling; triglyceride and diacylglycerol catabolic processes) along with detoxification and xenobiotic response terms, suggesting a cohesive theme around lipid metabolism and related detox pathways. Some other terms like biotin/antibiotic biosynthesis or cellulose catabolism appear peripheral, likely noise, but don\u2019t override the lipid/detox signal. Confidence: Medium","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000124","count":7},{"id":"GO:0019433","count":7},{"id":"GO:0009102","count":6},{"id":"GO:0017000","count":6},{"id":"GO:0042136","count":5}]},{"hash":"667861948051946264","title":"Nuclear Transcription and RNA Processing","description":"Proteins in this cluster are dominated by GO terms related to DNA-templated transcription, transcription elongation regulation, RNA processing (siRNA processing), and mRNA decay (nonsense-mediated decay), implying a coherent nuclear role in gene expression and RNA metabolism. Some terms about DNA replication and regulatory processes are present, but the overarching theme centers on transcription control and RNA processing within the nucleus.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1900035","count":2},{"id":"GO:0090084","count":2}]},{"hash":"1887784424774999373","title":"Unknown","description":"The top GO terms show a mix of RNA processing (chloroplast and mitochondrial rRNA processing), ribosome biogenesis, and cellular respiration, alongside unrelated processes like brain development, platelet activation, and epithelial proliferation. There is no single cohesive function uniting all proteins, so a concise, representative label cannot be determined.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061820","count":2},{"id":"GO:0030168","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0050679","count":2}]},{"hash":"720181941910207636","title":"Unknown","description":"Unknown","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0046677","count":4},{"id":"GO:0031126","count":3},{"id":"GO:0017001","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0090503","count":3}]},{"hash":"704662665473645031","title":"DNA transcription regulation","description":"This cluster\u2019s top terms are dominated by DNA-templated transcription and its regulation (GO:0006355 and GO:0006351), indicating a core function in transcription control. The remaining terms are more disparate (neuronal development, deubiquitination, ERAD-related, etc.), suggesting some collateral roles but a coherent primary theme around transcription regulation. ","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0035520","count":1},{"id":"GO:1904378","count":1},{"id":"GO:1900425","count":1}]},{"hash":"795293732956093206","title":"Skeletal Muscle Differentiation and Regeneration","description":"The GO terms show positive regulation of satellite cell activation, skeletal muscle differentiation, and skeletal muscle regeneration, plus calcium signaling relevant to muscle function and some cardiac muscle communication. This combination points to a muscle development/regeneration theme for the cluster, despite a few obsolete or non-specific terms.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":3},{"id":"GO:0051281","count":2},{"id":"GO:0070315","count":2},{"id":"GO:0033234","count":2},{"id":"GO:2001015","count":2}]},{"hash":"1988220215728123923","title":"Unknown","description":"The Top Terms are very diverse, spanning sugar and elastin catabolism, nematode molting and pharyngeal pumping, immune cytokine production, and general growth/migration. There is no clear, single functional theme tying these terms together, so a coherent label cannot be derived. ","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019391","count":1},{"id":"GO:0000272","count":1},{"id":"GO:0005990","count":1},{"id":"GO:0018996","count":1},{"id":"GO:0043050","count":1}]},{"hash":"803688943087692050","title":"Unknown","description":"The top GO terms cover a wide and seemingly unrelated mix, including protein folding, ER organization, mitochondrial translation, fatty acid catabolism, tRNA biosynthesis, development, and even an odd nylon catabolic process. Because there is no clear, cohesive biological function tying these proteins together, there isn\u2019t a single representative label beyond Unknown.","confidence":"","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006457","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0030901","count":2},{"id":"GO:0007029","count":2},{"id":"GO:0019876","count":2}]},{"hash":"1136144800798608285","title":"Mitochondrial lipid metabolism and energy signaling","description":"The cluster revolves around lipid biosynthesis (cardiolipin, phosphatidic acid), lipid catabolism, and mitochondrial dynamics (fusion), coupled with nutrient and energy signaling pathways (insulin, PPAR) and cellular response to nutrients, suggesting a cohesive theme of mitochondrial lipid metabolism and energy regulation.","confidence":"Medium","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010636","count":1},{"id":"GO:0030719","count":1},{"id":"GO:0048017","count":1},{"id":"GO:0032049","count":1},{"id":"GO:0006654","count":1}]},{"hash":"549657100489415087","title":"Ubiquitin-Mediated Immune Signaling and Cell Fate","description":"The terms cluster around ubiquitination processes (protein ubiquitination, ubiquitin-dependent catabolic pathways, K33-linked ubiquitination) and their regulatory roles in immune signaling (TLR, B cell receptor) as well as cell fate decisions (cell cycle regulation, apoptosis, necroptosis). This indicates a coherent function group centered on ubiquitin-mediated control of immune signaling and cell fate.","confidence":"High","size":28,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":6},{"id":"GO:0042787","count":5},{"id":"GO:0071157","count":5},{"id":"GO:0034121","count":5},{"id":"GO:0000122","count":5}]},{"hash":"1886070055593717443","title":"Oxidative detoxification and stress response","description":"The cluster is enriched for cellular oxidant detoxification, glutathione metabolic process, toxin catabolic process, and responses to toxic substances and ethanol, along with nucleotide-excision repair and starvation response. This combination suggests a core theme of managing oxidative damage and toxin exposure via glutathione-mediated detoxification and DNA repair, with related metabolic and calcium-signaling stress responses, indicating a cohesive detoxification/stress-response function.","confidence":"High","size":27,"edges":270,"triangles":1704,"max_degree":26,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":21},{"id":"GO:0006749","count":20},{"id":"GO:0006289","count":20},{"id":"GO:0009072","count":20},{"id":"GO:0009407","count":19}]},{"hash":"1582824030110285026","title":"DNA replication and chromatin regulation","description":"The cluster centers on processes related to the cell cycle and genome maintenance: centrosome cycle, DNA replication, telomere maintenance via recombination, nucleosome density/chromatin regulation, and transcription regulation at RNA Pol II promoters. These indicate a cohesive theme of DNA replication coupled with chromatin remodeling and chromosome maintenance, with a developmental signal likely reflecting proliferative contexts (embryonic morphogenesis). Confidence: High","confidence":"","size":27,"edges":78,"triangles":72,"max_degree":14,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007098","count":16},{"id":"GO:0010571","count":16},{"id":"GO:0000722","count":14},{"id":"GO:0006260","count":14},{"id":"GO:0048701","count":14}]},{"hash":"1892200410349688247","title":"Peroxisomal lipid catabolism","description":"The cluster is dominated by triglyceride and phospholipid catabolic terms (e.g., triglyceride catabolic process, triglyceride mobilization, phosphatidylcholine and phosphatidylethanolamine catabolism) and includes peroxisome-related activity (protein import into peroxisome matrix), together pointing to lipid breakdown/remodeling within peroxisomes. A few non-lipid terms appear peripheral, but the lipid-centric signals define the cluster\u2019s function.","confidence":"High","size":27,"edges":57,"triangles":33,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":3},{"id":"GO:0010898","count":2},{"id":"GO:0034638","count":2},{"id":"GO:0036153","count":2},{"id":"GO:0046338","count":2}]},{"hash":"198796154963918009","title":"Plant chromatin remodeling and hormone signaling","description":"The cluster is dominated by chromatin-related terms (rDNA heterochromatin formation, nucleosome assembly, chromatin remodeling) and plant hormone responses (abscisic acid, cytokinin, gibberellin), suggesting a linked function in chromatin dynamics regulated by hormonal signals. Viral process and DNA repair terms appear as secondary aspects of stress-related responses but do not define the core theme.","confidence":"Medium","size":27,"edges":21,"triangles":14,"max_degree":7,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0000183","count":12},{"id":"GO:0016032","count":10},{"id":"GO:0009737","count":9},{"id":"GO:0043044","count":9},{"id":"GO:0009736","count":9}]},{"hash":"1048905836141728056","title":"Diverse metabolic biosynthesis and xenobiotic catabolism","description":"Most frequent GO terms point to biosynthesis and breakdown of a wide range of compounds (antibiotics like clavulanic acid, bile acids, xanthine, naphthalene, herbicides like 2,4-D, carnitine, prostaglandin signaling, tissue homeostasis). This suggests a cluster of proteins involved in general metabolism and biotransformation rather than a single specific pathway, so a broad label capturing diverse metabolic and xenobiotic processing fits. ","confidence":"Medium","size":27,"edges":294,"triangles":1762,"max_degree":26,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0033050","count":7},{"id":"GO:0046300","count":7},{"id":"GO:0006151","count":7},{"id":"GO:0045329","count":7}]},{"hash":"612050113147538186","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":13,"triangles":0,"max_degree":10,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007568","count":9},{"id":"GO:0043547","count":9},{"id":"GO:0061158","count":8},{"id":"GO:1903883","count":8},{"id":"GO:0001519","count":8}]},{"hash":"2065509775175381529","title":"Signaling and cytoskeleton regulation","description":"This cluster is enriched for terms related to signal transduction (Ras and Rho pathways), protein dephosphorylation, and actin cytoskeleton organization, indicating a theme of signaling-driven cytoskeletal dynamics. Additional terms like mitochondrial fission, DNA repair, and glycolytic regulation reflect broader regulatory connections but do not redefine the main theme.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006470","count":3},{"id":"GO:0046580","count":3},{"id":"GO:0007605","count":3},{"id":"GO:0035023","count":3}]},{"hash":"1036869100823617638","title":"RNA processing and translational regulation","description":"This cluster is dominated by post-transcriptional control terms: translation initiation/reinitiation, miRNA/ncRNA-mediated silencing, spliceosome-regulated splicing, mRNA modification and stability under stress. Together, these point to a cohesive group of proteins involved in RNA maturation and translation control, with blastocyst formation likely reflecting developmental context or annotation noise.","confidence":"High","size":27,"edges":15,"triangles":1,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0001731","count":15},{"id":"GO:0002188","count":15},{"id":"GO:0031047","count":14},{"id":"GO:0048026","count":14},{"id":"GO:0010610","count":14}]},{"hash":"766895616631340494","title":"Keratinocyte differentiation and signaling regulation","description":"This cluster centers on epidermal differentiation and core signaling/transcriptional control modules, with GO terms for keratinocyte differentiation, Wnt/Hippo/TGF-\u03b2 signaling, and transcriptional regulation, plus apoptosis and defense responses that fit skin stress and cell-fate decisions. The common theme is epidermal cell fate dictated by signaling pathways and transcriptional programs.","confidence":"High","size":27,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0045944","count":7},{"id":"GO:0030512","count":6},{"id":"GO:0060044","count":6},{"id":"GO:0030216","count":6},{"id":"GO:0090263","count":6}]},{"hash":"356108659248074727","title":"Metal and Protein Stress Response","description":"The cluster's top GO terms converge on responses to metal ions (cadmium), unfolded protein stress, redox processes, and innate immunity, indicating a module tied to cellular stress management and damage repair. Although several terms are labeled obsolete, the shared themes point to metal-induced stress and protein quality control, with ancillary links to immune signaling and cell cycle regulation.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0071276","count":5},{"id":"GO:0000278","count":4},{"id":"GO:0045087","count":4},{"id":"GO:0051348","count":4}]},{"hash":"1357841389348500678","title":"Pheromone Response and Cell Division Control","description":"The cluster is enriched for GO terms such as response to pheromone, positive regulation of GTPase activity, mitotic cell cycle, cell division, and budding, which together point to signaling pathways that coordinate mating responses with growth and division through cytoskeletal regulation. While terms like cilium assembly or visual perception appear, they are less central to this core theme and may reflect broader annotations; the dominant signal is pheromone-induced signaling linked to cell cycle progression and budding. ","confidence":"Medium","size":27,"edges":325,"triangles":2377,"max_degree":26,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0019236","count":24},{"id":"GO:0043547","count":24},{"id":"GO:0000278","count":22},{"id":"GO:0007601","count":22},{"id":"GO:0060271","count":21}]},{"hash":"1655148340208440904","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061158","count":2},{"id":"GO:0030433","count":2},{"id":"GO:1903265","count":1},{"id":"GO:0010586","count":1},{"id":"GO:1903886","count":1}]},{"hash":"1897822543474769334","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":2},{"id":"GO:0061158","count":1},{"id":"GO:1904582","count":1},{"id":"GO:1904246","count":1},{"id":"GO:1904628","count":1}]},{"hash":"1860261005262146900","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":45,"triangles":0,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0039702","count":2},{"id":"GO:0015074","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0010587","count":2}]},{"hash":"1448466990246598400","title":"Mitotic spindle dynamics and ER-Golgi transport in development","description":"The cluster is dominated by mitosis-related terms (mitotic spindle assembly, mitotic cell cycle, tubulin complex assembly) and ER-to-Golgi vesicle transport, with additional development signals (brain and hippocampus, keratinocyte development, multicellular growth). This suggests a cohesive theme around cell division machinery coupled with secretory transport processes during developmental growth, rather than a single narrow function.","confidence":"Medium","size":27,"edges":140,"triangles":181,"max_degree":18,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0090307","count":6},{"id":"GO:0006888","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0007420","count":5},{"id":"GO:0021766","count":5}]},{"hash":"912107953884151182","title":"TLR signaling and innate immune defense","description":"The Top Terms are dominated by toll-like receptor signaling pathways (TLR2/3/9/10), MyD88-dependent signaling, and innate immune responses, including defense against viruses and regulation of inflammation. This indicates the cluster groups proteins involved in pathogen recognition and initiating innate immune responses via TLR signaling.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034162","count":2},{"id":"GO:0032741","count":2},{"id":"GO:0034166","count":2},{"id":"GO:0050729","count":2},{"id":"GO:0051770","count":2}]},{"hash":"1265715469858772546","title":"Broad-substrate membrane transporters","description":"The top GO terms point to transmembrane transport of a diverse set of substrates (vitamins, xenobiotics, various ions, glucose, nitrate, arabinose, urate), suggesting a cluster of membrane transporter proteins with broad substrate specificity. A single term about replicative senescence appears unrelated to transport and does not define the cluster\u2019s core function.","confidence":"High","size":27,"edges":42,"triangles":2,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":4},{"id":"GO:0006855","count":4},{"id":"GO:0035725","count":4},{"id":"GO:1904659","count":4},{"id":"GO:0071805","count":4}]},{"hash":"1107983098734053297","title":"Unknown","description":"The Top Terms are highly heterogeneous, spanning multiple metabolic biosynthetic processes, redox-related terms, metal stress response, and even developmental signals. With no edges or cohesive functional theme uniting the proteins, there isn\u2019t a clear shared function to label the cluster beyond Unknown.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009435","count":2},{"id":"GO:0006107","count":2},{"id":"GO:0042158","count":2},{"id":"GO:0006596","count":2}]},{"hash":"1890831748494802368","title":"Calcium Transport and Signaling in Muscle and Neurons","description":"The cluster centers on calcium ion transport and homeostasis (plasma membrane export/import and mitochondrial Ca2+ handling), with accompanying terms for regulation of skeletal and cardiac muscle contraction and synaptic plasticity (long-term potentiation). This suggests a cohesive module of calcium signaling that links ion transport to excitation-contraction coupling in muscles and calcium-dependent signaling in neurons, with ancillary ion transport processes aligned to this theme.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990034","count":4},{"id":"GO:0048022","count":3},{"id":"GO:0098735","count":3},{"id":"GO:0010163","count":3},{"id":"GO:0060291","count":3}]},{"hash":"28337153112326439","title":"Unknown","description":"Unknown","confidence":"","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0046835","count":5},{"id":"GO:0009236","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0006814","count":3}]},{"hash":"1189501840526695704","title":"Innate antiviral dsRNA response","description":"This cluster is dominated by GO terms for innate immune defense, including cellular response to type I interferon and to exogenous dsRNA, plus antiviral defense regulation. These patterns point to proteins involved in antiviral sensing and signaling pathways, with other terms like mitochondria distribution and GPCR signaling likely reflecting additional, less central roles orAnnotation breadth. Overall, the core function appears tied to innate antiviral responses.","confidence":"High","size":27,"edges":10,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045087","count":10},{"id":"GO:0071357","count":10},{"id":"GO:0051301","count":10},{"id":"GO:0050689","count":10},{"id":"GO:0071360","count":10}]},{"hash":"881557644760219307","title":"Unknown","description":"The top terms are heterogeneous, including obsolete RNA-processing terms and diverse developmental processes (DNA-templated transcription, ovarian follicle development, marginal zone B cell differentiation, meiotic division, root hair development), with no evident shared pathway or interaction (Edges: 0, Triangles: 0, Max Degree: 0). This lack of a coherent common function makes a specific, representative label inappropriate.","confidence":"","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:0070940","count":2},{"id":"GO:2000134","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0080147","count":2}]},{"hash":"345914956671623730","title":"Nematode Neurotransmission and Protein Regulation","description":"Based on the top terms, the cluster is enriched for protein homooligomerization and ubiquitination (protein regulation) alongside neurotransmitter transport (synaptic function). While a few nematode-specific processes (molting, cuticle) are present at low frequencies, the dominant themes point to nematode neuronal signaling and protein homeostasis. This suggests the cluster represents proteins involved in synaptic regulation and protein regulation in nematodes.","confidence":"High","size":27,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":13},{"id":"GO:0016567","count":12},{"id":"GO:0006836","count":9},{"id":"GO:2000372","count":9},{"id":"GO:0018996","count":2}]},{"hash":"892709179139294540","title":"Brain Neurotransmission and Stress Response","description":"The top GO terms cluster around brain neurotransmission and signaling (dopamine catabolic process, negative regulation of serotonin secretion, substantia nigra development) and responses to stress hormones and xenobiotics (response to corticosterone, response to xenobiotic stimulus, response to ethanol). This suggests a coherent theme of CNS neurotransmission modulated by stress and environmental compounds, with a few peripheral or obsolete terms present. ","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0043046","count":13},{"id":"GO:0009228","count":11},{"id":"GO:0014063","count":11},{"id":"GO:0051412","count":11},{"id":"GO:0042493","count":11}]},{"hash":"1655548701246511197","title":"Embryonic Development and Organogenesis","description":"This cluster is enriched for embryonic development terms: brain development, limb bud formation, neural crest cell migration, and broader multicellular organism development, plus digestive tract morphogenesis. It also includes DNA-templated transcription and TGF-beta signaling response, pointing to regulatory programs active during development. The lack of edges suggests the proteins contribute to a coordinated developmental process rather than forming dense interaction networks.","confidence":"High","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0071560","count":2},{"id":"GO:0060174","count":2},{"id":"GO:0006351","count":2}]},{"hash":"576167200549748629","title":"Sterol and glycosphingolipid biosynthesis and trafficking","description":"The top terms point to lipid metabolism, notably cholesterol metabolic process and glycosphingolipid biosynthesis (globoside, IPC), with additional signals of vesicle/ vacuolar transport and effects on cell shape polarity. Despite some obsolete annotations, the common theme appears to be lipid biosynthesis in the secretory/vesicular pathways coupled with membrane trafficking that can influence cell polarity.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008203","count":2},{"id":"GO:0018401","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0001576","count":1},{"id":"GO:0036210","count":1}]},{"hash":"813822176276981366","title":"Fructose-Glycolysis-PPP Metabolism","description":"The top GO terms indicate a strong focus on carbohydrate metabolism and energy production: fructose metabolism, glycolysis, fructose 2,6-bisphosphate regulation of glycolysis, carbohydrate phosphorylation, and regulation of the pentose phosphate pathway, with serine biosynthesis linked to glycolytic intermediates. While a couple terms (cellular response to cobalt ion, intestinal epithelial cell development) are less central, the core cluster appears to coordinate glycolytic flux and related pathways, justifying this label.","confidence":"Medium","size":27,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006000","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0043456","count":2},{"id":"GO:1904024","count":2},{"id":"GO:0006003","count":2}]},{"hash":"734009830158871766","title":"Actin-driven vesicle transport and migration","description":"The cluster shows a strong enrichment for actin-related processes: vesicle transport along actin filaments, actin nucleation, and migration-related signaling (VEGF pathways, cell gliding). Together with membrane raft distribution and secretory granule localization, these terms point to coordinated cytoskeletal remodeling and vesicle trafficking driving cell movement. Some terms (elastic fiber assembly, phagocytosis signaling) are related but secondary to the core actin/motility theme, reinforcing a broader connection to cytoskeletal organization and trafficking in motile, signaling-competent cells.","confidence":"High","size":26,"edges":248,"triangles":1355,"max_degree":25,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0044855","count":10},{"id":"GO:0031585","count":10},{"id":"GO:0030050","count":10},{"id":"GO:0038089","count":10},{"id":"GO:0051127","count":10}]},{"hash":"1661543097411878730","title":"Ubiquitin-Proteasome Regulation in Innate Immunity","description":"The cluster shows strong representation of ubiquitin-related processes (SCF-dependent proteasomal degradation, K33-linked ubiquitination, ERAD) and innate immune signaling (NOD2 pathway, NF-kappaB regulation, defense against Gram-positive bacteria, neutrophil activation modulation). While a few terms touch on muscle development or mitochondrial permeability, the dominant theme is ubiquitin-mediated protein turnover linked to immune signaling, suggesting proteins focused on proteostasis that modulate innate immune responses.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902564","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0048741","count":3},{"id":"GO:0046902","count":3},{"id":"GO:0030433","count":3}]},{"hash":"1731799521589037510","title":"Amino acid biosynthesis and metal ion transport","description":"This cluster shows enrichment for amino acid biosynthesis (proline, isoleucine, valine, tyrosine) and pantothenate, along with metal ion import (copper, iron) and NADPH regeneration, suggesting a metabolic module focused on amino acid/cofactor production and metal uptake. The presence of both biosynthetic and metal transport terms implies a cohesive metabolic theme rather than unrelated functions.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015677","count":3},{"id":"GO:0006740","count":3},{"id":"GO:0055129","count":2},{"id":"GO:0009097","count":2},{"id":"GO:0009099","count":2}]},{"hash":"1166679689741397901","title":"Ubiquitin-dependent proteolysis in antiviral immunity","description":"The top GO terms cluster around ubiquitin-dependent protein degradation and polyubiquitination, notably SCF-proteasome\u2013mediated pathways, with concurrent signals of innate immune activation (innate immune response, defense against virus, TLR9 signaling, and IFN-\u03b2 production). This suggests a functional group where ubiquitin-proteasome processes regulate antiviral innate immune signaling and transcriptional control related to immune responses.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:0000209","count":7},{"id":"GO:0031146","count":6},{"id":"GO:0000122","count":5},{"id":"GO:0045087","count":5}]},{"hash":"1058238273830156775","title":"Transmembrane Transporters for Ions and Metabolites","description":"Based on GO terms, this cluster is dominated by transmembrane transport of ions (phosphate, nitrate/nitrite, sodium) and small molecules (arabinos e, vitamins) plus related metabolic processes (fucose metabolism, nitrate assimilation), with an additional term for neurotransmitter loading into synaptic vesicles, pointing to vesicular transport as part of the shared function.","confidence":"High","size":26,"edges":131,"triangles":215,"max_degree":24,"top_function":"protein folding","top_go_terms":[{"id":"GO:0035435","count":7},{"id":"GO:0015706","count":6},{"id":"GO:0015751","count":6},{"id":"GO:0015707","count":6},{"id":"GO:0042891","count":6}]},{"hash":"1143942864805839065","title":"Steroid and xenobiotic metabolism","description":"This cluster is dominated by GO terms for xenobiotic transmembrane transport and steroid-related metabolism (androgen metabolic and catabolic processes, glucocorticoid biosynthesis), with an additional regulatory term on transcription. These together suggest a functional module involved in processing external compounds and steroid hormones, though some terms (like melanin biosynthesis and lung development) indicate broader metabolic roles. Confidence: Medium","confidence":"","size":26,"edges":5,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006855","count":4},{"id":"GO:0046677","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0008209","count":3},{"id":"GO:0006355","count":3}]},{"hash":"1027701322231960725","title":"Vesicle trafficking and lysosomal transport","description":"The cluster is dominated by GO terms tied to membrane trafficking and organelle transport, including ER-to-Golgi vesicle transport, late endosome to lysosome transport, lysosomal membrane organization, synaptic vesicle budding, and very-low-density lipoprotein particle assembly. These point to a common theme of intracellular trafficking and vesicle dynamics, with other terms like transcription regulation and apoptosis appearing as less central, likely peripheral associations. ","confidence":"Medium","size":26,"edges":41,"triangles":0,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:1902307","count":2},{"id":"GO:0033028","count":2},{"id":"GO:0097212","count":2},{"id":"GO:0007289","count":2}]},{"hash":"2014925787451471315","title":"Axonogenesis and Vestibular Morphogenesis","description":"This cluster is dominated by terms tied to neural development and inner-ear sensory structure formation, notably axonogenesis, semicircular canal morphogenesis, and vestibular reflex. The accompanying terms about regulation of translational initiation and protein kinase activity suggest broader signaling and protein synthesis control during development. Immune-related terms are present but less central to the overall theme. Overall, the proteins appear to cluster around neural-vestibular development with supportive regulatory roles.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007409","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0006446","count":2}]},{"hash":"2208901399643629770","title":"Membrane nutrient and ion transporters","description":"The top GO terms show transmembrane transport for a variety of substrates (nitrate, nitrite, phosphate, galactose, fucose, sodium, vitamins) and related transport processes, indicating a cluster of membrane transporter proteins with diverse substrates rather than a single specialized pathway. This common theme justifies labeling as membrane nutrient and ion transporters.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":3},{"id":"GO:0015707","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0006004","count":2},{"id":"GO:0015757","count":2}]},{"hash":"1495851098908389963","title":"Ciliary/Flagellar Motility and Intraflagellar Transport","description":"The top terms repeatedly reference cilium/flagellum movement, intraciliary retrograde transport, dynein arm assembly, and left/right symmetry, all of which point to a shared role in ciliary motility and the associated microtubule-based transport. Additional terms about ventricle development and sperm motility support this theme through ciliary functions in development and gamete movement.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051293","count":2},{"id":"GO:1990048","count":2},{"id":"GO:0072382","count":2},{"id":"GO:0034063","count":2},{"id":"GO:0003341","count":2}]},{"hash":"1151590053570392177","title":"Epigenetic Transcription Regulation","description":"This cluster centers on chromatin modification and transcription control, as indicated by GO terms for histone methylation (H4-K20), histone acetylation (H3-K27), and regulation of transcription by RNA polymerase II. Although some terms are obsolete or represent diverse biological contexts (heart development, IgA switching), the dominant signals point to epigenetic regulation of gene expression via chromatin modification and transcriptional control rather than downstream signaling pathways. ","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090309","count":1},{"id":"GO:0045605","count":1},{"id":"GO:0034772","count":1},{"id":"GO:0007507","count":1},{"id":"GO:0048298","count":1}]},{"hash":"1459560750443776252","title":"Metal ion transport and homeostasis","description":"The terms cluster around transport and detoxification of various metal ions (cadmium, zinc, manganese, iron, calcium) and maintaining intracellular metal balance, including transmembrane movement and detoxification processes. This cohesive pattern supports a label focused on metal ion transport and homeostasis.","confidence":"High","size":26,"edges":78,"triangles":41,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0098849","count":5},{"id":"GO:0006828","count":5},{"id":"GO:0098703","count":5},{"id":"GO:0010312","count":4},{"id":"GO:0055072","count":4}]},{"hash":"49235560845381967","title":"Diverse biosynthetic processes","description":"Most frequent GO terms point to biosynthesis of a variety of compounds (antibiotics, glucocorticoids, melanin, mycolic acids, acetoin), suggesting the cluster centers on diverse biosynthetic pathways rather than a single function. Additional terms like regulation of transcription and androgen metabolism are present but less cohesive with the core biosynthesis theme, implying a broad metabolic cluster. ","confidence":"Medium","size":26,"edges":3,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0055114","count":8},{"id":"GO:0008209","count":6},{"id":"GO:0006355","count":6},{"id":"GO:0006710","count":6}]},{"hash":"201168497837187120","title":"Mitochondrial lipid synthesis and remodeling","description":"The cluster is dominated by GO terms for lipid biosynthesis and mitochondrial lipid remodeling, including cardiolipin remodeling, ether lipid biosynthesis, CDP-diacylglycerol biosynthesis, triglyceride biosynthesis, and mitochondrial ATP synthesis, suggesting a cohesive function in mitochondrial lipid production and membrane lipid homeostasis. Some terms reflect broader developmental contexts (e.g., cerebellum morphogenesis), but the lipid-centric pattern remains the core theme.","confidence":"High","size":26,"edges":38,"triangles":15,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0021587","count":11},{"id":"GO:0042775","count":11},{"id":"GO:0019432","count":11},{"id":"GO:0002071","count":11},{"id":"GO:0010143","count":11}]},{"hash":"1444869697989635245","title":"Unknown","description":"The GO terms for this cluster span diverse processes (regulation of fatty acid biosynthesis, cell cycle/division, transcription regulation, stress responses like cadmium exposure, viral processes, and biosynthesis pathways such as lipopolysaccharide and phenylacetate catabolism), with no clear, unifying function emerging. This lack of a coherent theme makes a concise, specific label unreliable.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045717","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0045892","count":3},{"id":"GO:0046686","count":2}]},{"hash":"2188728031969088881","title":"Triglyceride and phospholipid catabolism","description":"The top GO terms are dominated by triglyceride catabolic processes, triglyceride mobilization, and phospholipid (phosphatidylcholine and phosphatidylethanolamine) catabolism/remodeling, indicating a lipid breakdown and membrane lipid remodeling theme; a few terms about PKA regulation or synapse organization are present but secondary.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":2},{"id":"GO:0010898","count":1},{"id":"GO:0034638","count":1},{"id":"GO:0019433","count":1},{"id":"GO:0036153","count":1}]},{"hash":"37433097471784196","title":"Mitochondrial Dynamics and Endocytic Recycling","description":"This cluster is enriched for mitochondrial-related processes (fission, membrane organization, inheritance, distribution) and endocytic recycling, pointing to a shared theme of organelle dynamics and vesicle trafficking. The presence of GABAergic synaptic transmission suggests neuronal vesicle cycling, while ribosomal export and cell cycle terms appear as broader housekeeping annotations, providing less central support for the main theme.","confidence":"Medium","size":26,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032456","count":4},{"id":"GO:0000266","count":3},{"id":"GO:0051932","count":3},{"id":"GO:0000055","count":3},{"id":"GO:0048312","count":3}]},{"hash":"1581155962757232271","title":"GPCR-cGMP Signaling","description":"The GO terms cluster around G protein-coupled receptor signaling (adenosine/adrenergic receptors) and receptor guanylyl cyclases, coupled with cGMP biosynthesis and signaling, which together point to a GPCR-driven pathway that culminates in cGMP production\u2014consistent with NO/cGMP signaling and related phototransduction contexts. Some terms are broader or obsolete, but the dominant theme is GPCR-mediated cGMP signaling.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0071880","count":1},{"id":"GO:0052565","count":1},{"id":"GO:0009785","count":1},{"id":"GO:0070483","count":1}]},{"hash":"1514796565797028697","title":"ER Stress Response and Protein Folding","description":"Based on the top GO terms, the cluster is enriched for endoplasmic reticulum\u2013associated processes: response to ER stress and protein folding in the ER. These signals point to chaperones and folding-related proteins tied to the unfolded protein response. Although there are some transcription regulation and viral process terms present, the strongest and most coherent theme is ER homeostasis and protein folding.","confidence":"High","size":26,"edges":7,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0033158","count":3},{"id":"GO:0034976","count":3},{"id":"GO:0006662","count":3},{"id":"GO:0043388","count":3}]},{"hash":"415065814650777116","title":"Unknown","description":"Unknown","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0071039","count":2},{"id":"GO:0034473","count":2},{"id":"GO:0071035","count":2},{"id":"GO:0034476","count":2}]},{"hash":"2048152003899694839","title":"Bacterial DNA replication and cell division","description":"The top terms cluster around core bacterial cell-cycle processes\u2014DNA replication and recombination, and FtsZ-dependent cytokinesis (with sporulation mentioned)\u2014alongside related metabolism like iron/copper transport and cellulose degradation, which fits a bacterial lifestyle. The cohesion is moderate given some peripheral terms, but the recurring theme is genome maintenance and division machinery.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0006825","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0030435","count":1}]},{"hash":"767319961190491386","title":"N-terminal and histone acetylation","description":"The majority of top GO terms describe acetylation events\u2014especially N-terminal protein acetylation and histone H4 acetylation (plus related peptidyl acetylations)\u2014indicating a cohesive group of proteins involved in acetyltransferase activity or acetylation regulation; some terms may be incidental annotations.","confidence":"High","size":26,"edges":302,"triangles":2118,"max_degree":25,"top_function":null,"top_go_terms":[{"id":"GO:0061606","count":25},{"id":"GO:0018002","count":25},{"id":"GO:0043967","count":25},{"id":"GO:0030187","count":25},{"id":"GO:0006348","count":25}]},{"hash":"1171264850072048755","title":"Male Meiosis I Chromatid Cohesion","description":"The terms cluster around meiosis in male germ cells, especially sister chromatid cohesion during meiosis I, with related chromatin localization and telomere dynamics, plus seminiferous tubule development and fertilization signaling that fit the broader germ cell development context.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045876","count":1},{"id":"GO:0010032","count":1},{"id":"GO:0007141","count":1},{"id":"GO:0034087","count":1},{"id":"GO:0072520","count":1}]},{"hash":"408640005696149988","title":"Chromatin remodeling and transcription regulation","description":"The top GO terms are dominated by chromatin-related processes (chromatin remodeling, nucleosome assembly, and negative regulation of transcription by RNA polymerase II), suggesting a shared role in chromatin dynamics and transcription control. A spindle assembly term and a few plant/neuronal terms appear as minor associations, but the core signal points to chromatin regulation as the defining function of this cluster.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0006334","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0048709","count":2}]},{"hash":"1880399497613436262","title":"Sphingolipid biosynthesis and membrane organization","description":"This cluster centers on sphingolipid biosynthesis terms (globoside biosynthetic process; mannosyl-inositol phosphorylceramide biosynthetic process) and membrane-related processes (nuclear membrane organization, protein stabilization, synapse organization), suggesting a membrane lipid metabolism and organization theme. Developmental signaling terms (Wnt signaling, cardiac muscle growth) are present but less representative, so the core theme remains lipid biosynthesis and membrane dynamics.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090263","count":2},{"id":"GO:0071763","count":1},{"id":"GO:0001576","count":1},{"id":"GO:0036210","count":1},{"id":"GO:0051999","count":1}]},{"hash":"1422107086722538930","title":"Ubiquitin-Proteasome and PTM Regulation","description":"The top GO terms cluster around ubiquitin-dependent protein catabolism via the SCF proteasome pathway, along with reversible post-translational modifications (deneddylation and desumoylation) that influence chromatin binding and cell-cycle processes (kinetochore assembly, endoreduplication). This points to a cohesive theme of proteostasis linked to chromatin regulation through PTMs, even though a few immune-related terms appear. Overall, the cluster seems to coordinate protein turnover with chromatin/cell-cycle control through PTMs.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0043086","count":2},{"id":"GO:0032875","count":1},{"id":"GO:0000338","count":1}]},{"hash":"459684978925628946","title":"Unknown","description":"The top GO terms are highly heterogeneous, ranging from sensory perception and muscle/fat differentiation to plant-specific metabolism and stress responses, with no clear shared biological function tying the proteins together. This makes a single, intuitive label unreliable.","confidence":"","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":2},{"id":"GO:0014902","count":2},{"id":"GO:0045493","count":2},{"id":"GO:0006144","count":2},{"id":"GO:0051301","count":2}]},{"hash":"117155403001513582","title":"Wnt-driven Development and Morphogenesis","description":"The terms cluster around developmental signaling and morphogenesis, especially Wnt signaling linked to midbrain development, pancreas morphogenesis, and multicellular growth, with supporting signals from transcriptional regulation and ECM remodeling. A few inflammatory cytokine terms are present but likely reflect remodeling processes rather than a separate pathway. Overall, the theme is developmental signaling and tissue morphogenesis.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0030901","count":4},{"id":"GO:0016055","count":4},{"id":"GO:0045415","count":3},{"id":"GO:0050720","count":3}]},{"hash":"1406422962514028833","title":"Membrane Ion Transport and Homeostasis","description":"The top GO terms cluster around transmembrane transport of ions (K+, Na+) and xenobiotics, membrane potential dynamics (hyperpolarization and repolarization), and cell volume homeostasis, pointing to a set of ion transporters/channels and related membrane regulators. This justifies labeling as membrane ion transport and homeostasis, reflecting the shared function of moving ions across membranes to regulate membrane potential and cellular balance. ","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060081","count":2},{"id":"GO:0071805","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0050976","count":2},{"id":"GO:0030007","count":2}]},{"hash":"293289125817179985","title":"Eye Development and Visual Perception","description":"The top GO terms are strongly centered on visual perception and retina development, indicating an eye/retina-focused function for this cluster. While there are a few regulatory and general processes (e.g., transcription regulation, kinase activity) represented, they do not outweigh the eye-related theme. A concise label that captures the dominant signal is Eye Development and Visual Perception.","confidence":"High","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":3},{"id":"GO:0006469","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0032715","count":2},{"id":"GO:0006366","count":2}]},{"hash":"1796132300651029608","title":"Biosynthesis of vitamins, polyamines, and proteoglycans","description":"This cluster is enriched for diverse biosynthetic processes (biotin, cobalamin, polyamines, antibiotics, and proteoglycan/glycosaminoglycan biosynthesis), with a separate note on xenobiotic response. The lack of interactions (edges) suggests proteins span multiple biosynthetic roles rather than a single pathway, so the label reflects a broad biosynthetic theme rather than a precise function.","confidence":"Medium","size":26,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0006596","count":4},{"id":"GO:0009236","count":4},{"id":"GO:0017000","count":4}]},{"hash":"2125338694731191873","title":"Ubiquitin-Dependent Protein Degradation and Stress Responses","description":"This cluster is enriched for ubiquitin-related processes (ubiquitin-dependent SMAD catabolic process, protein autoubiquitination, ERAD pathways) and a variety of stress-response terms (response to cold, lipopolysaccharide, chitin, ethanol, ABA-related regulation). The common theme is ubiquitin-mediated protein quality control occurring during diverse stress conditions, grouping these proteins into a stress-response/protein-degradation module.","confidence":"High","size":25,"edges":8,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030579","count":7},{"id":"GO:0055114","count":7},{"id":"GO:0032496","count":7},{"id":"GO:0009409","count":7},{"id":"GO:0051865","count":6}]},{"hash":"948273356630943185","title":"Nucleic Acid Metabolism and Ribosome Biogenesis","description":"This cluster shows strong signals for DNA replication and SOS response, suggesting genome maintenance involvement, alongside RNA processing and ribosome biogenesis terms (rRNA maturation, ribosomal subunit biogenesis, spliceosomal disassembly, RNA exon ligation, mitochondrial ribosome assembly). The combination points to a theme of nucleic acid metabolism coupled with ribosome assembly across nuclear/mitochondrial contexts.","confidence":"Medium","size":25,"edges":22,"triangles":7,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009432","count":16},{"id":"GO:0006268","count":16},{"id":"GO:0006260","count":15},{"id":"GO:1902775","count":13},{"id":"GO:0000390","count":13}]},{"hash":"1539418443105490399","title":"Organelle proteostasis and ribosome assembly","description":"The top GO terms point to chloroplast and mitochondrial processes (chloroplast organization, plastid rRNA transcription, mitochondrial ribosome assembly, cytochrome complex assembly) along with proteostasis and redox-related terms (response to unfolded protein, cell redox homeostasis, detoxification). This pattern suggests a shared function in maintaining organelle protein folding, maturation, and ribosome biogenesis, as well as redox balance within chloroplasts and mitochondria. Some terms appear peripheral, but the core theme is organelle proteostasis and ribosome assembly.","confidence":"Medium","size":25,"edges":60,"triangles":19,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0055114","count":1},{"id":"GO:0098869","count":1},{"id":"GO:0042158","count":1}]},{"hash":"2124862306449907763","title":"Ubiquitin-Dependent Proteolysis","description":"The cluster is dominated by GO terms for ubiquitin tagging and proteasome-mediated protein breakdown (ubiquitin-dependent catabolic process, polyubiquitination, autoubiquitination, SCF-dependent pathway, and K48-linked ubiquitination). This points to coordinated function in targeted protein degradation via the ubiquitin-proteasome system, with some regulatory links to signaling pathways like Wnt and growth control. Peroxisomal import appears ancillary.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0030433","count":6},{"id":"GO:0031146","count":5},{"id":"GO:0000209","count":5},{"id":"GO:0051865","count":5}]},{"hash":"1591101908368201146","title":"Membrane nutrient and xenobiotic transporters","description":"This cluster is dominated by transmembrane transport GO terms for nutrients and xenobiotics (vitamins, D-glucose, xenobiotic substrates), with supportive signals for related trafficking (Golgi to lysosome) and nutrient response. The data point to a group of membrane transporters and nutrient-uptake/processing proteins rather than a single catalytic function, with some regulatory/trafficking components included. ","confidence":"High","size":25,"edges":15,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0035461","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0006855","count":2}]},{"hash":"183474901626454850","title":"Hormone and lipid metabolism with development","description":"Despite some heterogeneity (detox metabolism terms), the strongest shared signal is metabolism of lipid-derived hormones (prostaglandin biosynthesis, bile acid biosynthesis, vitamin D catabolism, androgen metabolism) together with developmental processes (digestive tract development, female gonad development, tongue muscle differentiation). This suggests a core theme around hormone/lipid metabolism linked to developmental regulation, hence the chosen label.","confidence":"Medium","size":25,"edges":11,"triangles":5,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001516","count":4},{"id":"GO:0033076","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0048565","count":3},{"id":"GO:0042369","count":3}]},{"hash":"1679513685697514795","title":"Neuronal synaptic trafficking and signaling","description":"This cluster centers on neuronal endosome trafficking and synaptic signaling. Top terms include receptor recycling, regulation of endosome size, glutamatergic neurotransmission, neurotransmitter transport, and Rho-mediated signaling, all pointing to coordinated trafficking and communication at synapses. While there are also terms related to transcription regulation and histone methylation, they appear less central to the dominant synaptic trafficking theme. Therefore, the label reflects the core function of the proteins in synaptic trafficking and signaling.","confidence":"High","size":25,"edges":43,"triangles":37,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0035023","count":9},{"id":"GO:0060316","count":9},{"id":"GO:0001881","count":8},{"id":"GO:0051036","count":8},{"id":"GO:0035249","count":8}]},{"hash":"1384261403800140381","title":"Unknown","description":"The top GO terms are a disparate mix of processes (actin nucleation regulation, invasive growth under glucose limitation, rRNA maturation, membrane protein insertion, outer membrane assembly, various metabolic processes) with only a couple of mappings per term and no clear common function. This lack of a cohesive theme makes it hard to assign a meaningful, specific label beyond Unknown.","confidence":"","size":25,"edges":5,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:2000601","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0000463","count":2},{"id":"GO:0000466","count":2},{"id":"GO:0032515","count":1}]},{"hash":"871667117986078591","title":"Lymphocyte Receptor Signaling and Proliferation","description":"The cluster\u2019s top GO terms center on B cell and T cell receptor signaling, along with cell surface receptor serine/threonine kinase pathways and VEGF receptor signaling, plus DNA replication and cell cycle processes. This combination suggests a coherent theme of receptor-mediated immune signaling driving cell proliferation, which best fits a label focusing on lymphocyte receptor signaling and subsequent proliferation.","confidence":"High","size":25,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0022038","count":16},{"id":"GO:0050853","count":16},{"id":"GO:0007178","count":16},{"id":"GO:0033138","count":16},{"id":"GO:0010571","count":16}]},{"hash":"2253384226299616599","title":"Innate antiviral signaling and ubiquitin regulation","description":"Based on the top GO terms, the proteins are enriched for innate immune functions and antiviral defense (innate immune response, defense response to virus, NOD2 signaling). The presence of ubiquitination-related terms suggests regulation of protein turnover linked to immune signaling (protein ubiquitination, ubiquitin-dependent protein catabolic process). A few terms note vitamin D response and regulatory transcription/cell cycle processes, but the dominant pattern centers on innate immune sensing and ubiquitin-mediated regulation.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0051607","count":5},{"id":"GO:0033280","count":5},{"id":"GO:0016567","count":4},{"id":"GO:0042787","count":4}]},{"hash":"1020492975714435368","title":"Ubiquitin-Proteasome Regulation of Innate Immunity","description":"This cluster centers on ubiquitin-dependent protein degradation (ubiquitination; SCF-dependent pathways) and proteasomal turnover, coupled with antiviral/innate immune signaling (defense response to virus, innate immune response, TLR signaling regulation). The inclusion of cell cycle, transcriptional, apoptotic, and necroptotic regulation aligns with ubiquitin-mediated control over these processes. Together, the dominant theme is proteasome- and ubiquitin-driven regulation of antiviral immunity and related cellular pathways.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":6},{"id":"GO:0000209","count":5},{"id":"GO:0031146","count":3},{"id":"GO:0051607","count":3},{"id":"GO:0045087","count":3}]},{"hash":"2111614153166220835","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034965","count":2},{"id":"GO:1905267","count":2},{"id":"GO:0000294","count":2},{"id":"GO:0001682","count":2},{"id":"GO:0006412","count":2}]},{"hash":"802102776244628367","title":"Glycosylation and amino acid transport","description":"The top GO terms cluster around cellular processing and transport: dolichol-linked oligosaccharide biosynthesis (N-linked glycosylation), several amino acid and sugar transport/export processes, and amino acid homeostasis. A few immune-related terms appear but are sparse, suggesting the dominant theme is protein processing and nutrient transport rather than a single, cohesive immune function. Confidence: Medium","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006488","count":1},{"id":"GO:0007625","count":1},{"id":"GO:0002088","count":1},{"id":"GO:1904659","count":1},{"id":"GO:0034488","count":1}]},{"hash":"519519962175558784","title":"Transmembrane Transporters","description":"A cluster whose GO terms are all transmembrane transport processes across a wide range of substrates (vitamins, ions, nitrate/nitrite, arabinose, xenobiotics, phosphate). This consistency indicates membrane transporter activity as the shared function of these proteins.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":17},{"id":"GO:0071805","count":17},{"id":"GO:0006855","count":17},{"id":"GO:0015706","count":16},{"id":"GO:0015751","count":16}]},{"hash":"1062916811418963230","title":"Plant development and chloroplast organization","description":"These GO terms point to plant-specific biology: sieve element differentiation and pollen exine formation indicate reproductive and vascular development; shoot apical meristem regulation reflects vegetative/meristem development; chloroplast organization and high-light response tie to organelle function and photoadaptation. A couple of transport terms into Golgi hint at secretory pathways common to plant cells, but the dominant theme is plant development and chloroplast-related processes. Confidence: Medium","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008292","count":1},{"id":"GO:0090603","count":1},{"id":"GO:0061526","count":1},{"id":"GO:0009644","count":1},{"id":"GO:0009658","count":1}]},{"hash":"102559501820999684","title":"Eye development and photoreceptor maintenance","description":"This cluster is dominated by vision-related terms: camera-type eye development, photoreceptor cell maintenance, detection of light stimulus, and ciliary localization of receptors, all pointing to retina/photoreceptor biology and eye formation. A few outlier terms (e.g., galactose metabolism) are present but do not override the clear eye/vision theme.","confidence":"High","size":25,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006012","count":2},{"id":"GO:0050908","count":1},{"id":"GO:0045494","count":1},{"id":"GO:0031076","count":1},{"id":"GO:0097500","count":1}]},{"hash":"204918202588530050","title":"Lipid Metabolism and Endocannabinoid Signaling","description":"Top GO terms are centered on lipid metabolism and lipid-derived signaling (triglyceride and phosphatidylserine catabolism, cholesterol biosynthesis, and regulation of endocannabinoid signaling). This points to a cohesive theme of lipid turnover and lipid-mediated signaling, with additional terms related to detox/oxidative stress (response to toxic substance) and oxidation-reduction activity that often accompany metabolic remodeling. A few entries (sodium transport, antibiotic biosynthesis) are less directly connected and may reflect broader cellular contexts or incidental associations.","confidence":"Medium","size":25,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":7},{"id":"GO:0009636","count":6},{"id":"GO:0055114","count":5},{"id":"GO:2000124","count":4},{"id":"GO:0006660","count":4}]},{"hash":"302983445055398314","title":"Metabolism and Signaling Regulators","description":"Cluster proteins show enrichment for several biosynthetic processes (biotin biosynthesis, protoporphyrinogen IX biosynthesis, L-lysine biosynthesis and catabolic routes, L-alanine catabolism), indicating metabolic enzyme activities. At the same time, terms related to transcription (DNA-templated transcription) and signaling/regulatory pathways (Notch signaling pathway, cellular response to insulin stimulus) suggest roles in gene regulation and cellular signaling. Taken together, this cluster appears to group proteins involved in core metabolism alongside regulatory signaling processes, rather than a single cohesive pathway.","confidence":"Medium","size":25,"edges":271,"triangles":1753,"max_degree":24,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0019878","count":8},{"id":"GO:0009102","count":7},{"id":"GO:0042853","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0006782","count":7}]},{"hash":"1975812312440857529","title":"Golgi-glycosylation and sugar transport in plant roots","description":"This cluster centers on Golgi-localized sugar transport (UDP-glucose, GDP-fucose, etc.) and fucosylation glycosylation pathways (N- and O-linked), with plant root development terms (root hair and lateral roots) indicating a plant-specific role in root biology. The combination suggests a cohesive function in Golgi-based glycosylation and sugar trafficking within roots.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035584","count":2},{"id":"GO:0035436","count":2},{"id":"GO:0036071","count":2},{"id":"GO:0015713","count":2},{"id":"GO:0015786","count":2}]},{"hash":"1250494937843250908","title":"Synaptic Transmission and Plasticity","description":"This cluster is dominated by GO terms tied to neuronal signaling and synaptic function\u2014long-term potentiation, neurotransmitter release, calcium-responsive signaling, and dendrite extension\u2014pointing to roles in synaptic transmission and plasticity. Some terms (like abscisic acid signaling) are likely off-target noise, but the overall theme centers on neuronal communication and structural plasticity.","confidence":"Medium","size":25,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006646","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0043065","count":2},{"id":"GO:0007269","count":2},{"id":"GO:0035023","count":2}]},{"hash":"685030651477553551","title":"Synaptic signaling and membrane trafficking regulation","description":"A neuronal signaling theme is suggested by glutamatergic transmission, long-term potentiation, and regulation of synaptic plasticity. The presence of membrane-related terms (phosphatidylinositol dephosphorylation and vesicle-mediated cholesterol transport) supports a link to vesicle trafficking and membrane dynamics at synapses. While there are some terms related to ribophagy and RNA export, the dominant signal points to synaptic function coupled with membrane trafficking. Confidence: Medium","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035249","count":3},{"id":"GO:0034517","count":2},{"id":"GO:0060291","count":2},{"id":"GO:0031914","count":2},{"id":"GO:0060304","count":2}]},{"hash":"1889821361139290685","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035335","count":1},{"id":"GO:0030389","count":1},{"id":"GO:0006417","count":1},{"id":"GO:0009615","count":1},{"id":"GO:0006412","count":1}]},{"hash":"19459635397716109","title":"Unknown","description":"Unknown","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0016973","count":3},{"id":"GO:0042273","count":3},{"id":"GO:0006355","count":3},{"id":"GO:0006412","count":2}]},{"hash":"1460575137298157682","title":"Ubiquitin-Mediated Proteostasis and Stress Response","description":"The enrichment centers on ubiquitin-related processes (K11-linked ubiquitination), ER-associated degradation, and unfolded protein response, plus stress/immune signals such as cellular response to interferon-alpha and dsRNA. Despite some obsolete GO terms, the common thread is proteostasis via ubiquitin tagging and stress-induced responses, which together reflect a proteostasis/immune-stress module.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0006478","count":4},{"id":"GO:0051348","count":4},{"id":"GO:1903071","count":4},{"id":"GO:0035457","count":4}]},{"hash":"2102511608941093059","title":"Cell cycle and translation regulation","description":"The top GO terms cluster around cell division (meiotic and mitotic processes) and development, with translation-related processes (tRNA processing, hypusine biosynthesis) and proliferation control signals (negative regulation of fibroblast proliferation). This suggests a theme of coordinating cell proliferation with protein synthesis, i.e., cell cycle control linked to translational regulation.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048147","count":2},{"id":"GO:0007275","count":2},{"id":"GO:2001241","count":1},{"id":"GO:1903538","count":1},{"id":"GO:0007143","count":1}]},{"hash":"1828956501320419630","title":"Cell Cycle: Cohesion and Chromosome Segregation","description":"The cluster is dominated by GO terms tied to cell division, DNA replication, and, notably, sister chromatid cohesion and separation (biorientation, mitotic separation, meiotic cohesion). While other terms like ER-Golgi transport and transcription regulation appear, the core signal points to chromosome dynamics during cell division as the defining theme of this group.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0006283","count":3},{"id":"GO:0019079","count":2}]},{"hash":"771665861217454595","title":"Unknown","description":"The top GO terms span transcription regulation, phosphorylation, amino acid biosynthesis and salvage, stress responses, cell division, rDNA maintenance, and even behavioral terms, with no clear unifying function or pathway. This appears to be a heterogeneous set rather than a cohesive functional cluster, so a single intuitive label isn\u2019t warranted.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0016310","count":2},{"id":"GO:0019509","count":2},{"id":"GO:0009088","count":2},{"id":"GO:0019284","count":2}]},{"hash":"2056905924221900400","title":"Chromatin remodeling and heterochromatin maintenance","description":"The strongest signals are chromatin remodeling and rDNA heterochromatin formation, with related genome stability themes such as replication-born double-strand break repair and telomere-associated regulation. While some terms (viral process, gibberellin response) seem less connected, the core cluster centers on chromatin dynamics and genome maintenance.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0000183","count":5},{"id":"GO:0043044","count":5},{"id":"GO:0009739","count":4},{"id":"GO:1900033","count":4},{"id":"GO:1990414","count":4}]},{"hash":"2275185683544823904","title":"Unknown","description":"The top GO terms span unrelated areas such as pituitary development, transcription regulation, hormone biosynthesis, erythrocyte differentiation, thiamine biosynthesis, aging, stem cell proliferation, neuron maturation, and even camphor catabolism, with no single, coherent biological theme linking the cluster. This scattered functional profile suggests the cluster cannot be reliably assigned a specific biological function beyond Unknown.","confidence":"","size":25,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0021983","count":6},{"id":"GO:0055114","count":5},{"id":"GO:0000122","count":5},{"id":"GO:0046886","count":3},{"id":"GO:0045648","count":3}]},{"hash":"2040147691873166271","title":"Cell Wall Biosynthesis and Remodeling","description":"This cluster shows a consistent emphasis on cell wall-related processes: peptidoglycan biosynthesis and turnover, xylan/cellulose catabolic activities, and cell wall organization, with additional hints toward cell division and cell cycle that align with growth. While an outlier like insulin stimulus exists, the dominant theme is cell wall construction and remodeling.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":2},{"id":"GO:0045493","count":2},{"id":"GO:0016540","count":2},{"id":"GO:0030245","count":1},{"id":"GO:0071555","count":1}]},{"hash":"497418384825658267","title":"Brassinosteroid biosynthesis and plant lipid metabolism","description":"The top GO terms cluster around brassinosteroid biosynthesis and homeostasis, wax and very long-chain fatty acid biosynthesis, and dolichol-linked oligosaccharide biosynthesis, all pointing to plant-specific hormone production and cuticle lipid pathways. The presence of trichome branching further supports a plant epidermal/lipid metabolism theme. While some terms like progesterone/androgen biosynthesis are broader, the predominant signals align with plant brassinosteroid signaling and lipid metabolism, giving a high-confidence, specific cluster label.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006488","count":2},{"id":"GO:0010091","count":2},{"id":"GO:0010268","count":2},{"id":"GO:0030540","count":2},{"id":"GO:0030497","count":2}]},{"hash":"710084511070644831","title":"RNA and Protein Methyltransferases","description":"The top GO terms cluster around methylation activities: mRNA capping with 7-methylguanosine, guanine-N7 methylation, tRNA wobble uridine modification, histone H4 methylation, and various peptidyl- and N-terminal methylations. These point to enzymes that transfer methyl groups onto RNA or proteins, suggesting a common functional theme of methyltransferase activity across nucleic acids and proteins in these proteins, with some metabolic context terms reflecting bacterial biosynthetic processes. Confidence is High.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0006370","count":8},{"id":"GO:0036265","count":8},{"id":"GO:0046690","count":8},{"id":"GO:0009877","count":8}]},{"hash":"1783183178761782478","title":"Unknown","description":"The proteins appear to participate in a broad set of processes across domains (cytoskeletal dynamics, transcription, nutrient response, protein quality control, metabolism, flagellar organization, RNA modification, and plant-specific senescence), with no single cohesive function tying the GO terms together. Hence a specific, representative label is not evident.","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051013","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0030433","count":2}]},{"hash":"1078556497522569745","title":"Organelle RNA processing and respiration","description":"Most of the top GO terms point to chloroplast and mitochondrial RNA processing and cellular respiration, indicating a cluster of proteins involved in organelle gene expression and energy metabolism. Some peripheral terms related to adipocyte differentiation and signaling appear noisy or unrelated to the main theme. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901259","count":3},{"id":"GO:0000963","count":3},{"id":"GO:0045333","count":3},{"id":"GO:1902775","count":3},{"id":"GO:0090501","count":1}]},{"hash":"796480861408063851","title":"Unknown","description":"The terms span neural/muscular development (spinal cord motor neuron differentiation, neuromuscular movement), growth signaling (IGF receptor signaling), gene expression control (post-transcriptional gene silencing, mRNA destabilization), cell cycle/checkpoint signaling, tissue homeostasis, and basic transport (nitrite and phosphate). With 25 proteins and no observed edges, there isn't a single coherent function tying all terms together, so a specific, concise label isn\u2019t supported. Therefore, Unknown. ","confidence":"","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021522","count":1},{"id":"GO:0050885","count":1},{"id":"GO:0031571","count":1},{"id":"GO:0050881","count":1},{"id":"GO:0016441","count":1}]},{"hash":"1960555320415337471","title":"Brain and Multicellular Development","description":"These proteins show strong association with brain- and multicellular organism development (forebrain development, brain development, skeletal morphogenesis) and developmental regulation, with additional hints of transcriptional and translational control and protein turnover\u2014together pointing to a developmental-regulatory module rather than a single metabolic pathway.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0001731","count":4},{"id":"GO:0006349","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0007275","count":4}]},{"hash":"2182540859975990608","title":"Plant organellar RNA editing and translation regulation","description":"The top GO terms point to processes in plant organelles, especially chloroplasts and mitochondria: RNA editing (cytidine to uridine), mitochondrial translation regulation, and mitochondrial mRNA modification, plus chloroplast-nucleus signaling. The plant-specific terms like glucosinolate catabolism and seed dormancy hint at broader plant context but align with a plant organelle-centric theme.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019762","count":2},{"id":"GO:0060384","count":2},{"id":"GO:0098703","count":2},{"id":"GO:0090502","count":1},{"id":"GO:0000961","count":1}]},{"hash":"1694479109702158676","title":"Transcription Regulation and Chromatin Remodeling","description":"The top GO terms are dominated by negative regulation of transcription by RNA polymerase II and chromatin remodeling, pointing to a core function in controlling gene expression. The presence of development- and tissue-related terms (CNS development, innervation, glomerular development) suggests regulatory roles across different contexts, rather than a single tissue-specific function. The network shows no observed edges, though some proteins were re-added by predictive methods, consistent with regulatory rather than direct physical interactions. ","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0043044","count":2},{"id":"GO:0090305","count":2},{"id":"GO:0032836","count":2},{"id":"GO:0003094","count":2}]},{"hash":"655438188127422388","title":"Photosynthesis Light Harvesting and Photoprotection","description":"This cluster centers on light-driven processes: photosynthesis, light harvesting in photosystem II, and responses to various light conditions (high/low/red/UV-A). The presence of nonphotochemical quenching and phytol biosynthesis terms further points to chlorophyll-related light capture and photoprotection mechanisms.","confidence":"High","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048016","count":2},{"id":"GO:0071486","count":2},{"id":"GO:0009645","count":2},{"id":"GO:0018298","count":2},{"id":"GO:1904964","count":2}]},{"hash":"2010486707167109137","title":"Mitochondrial energy metabolism and insulin signaling","description":"The top GO terms are strongly centered on mitochondria: regulation of membrane permeability and membrane potential, mitochondrial ATP transmembrane transport, and magnesium ion export from mitochondrion, plus alpha-ketoglutarate transport. In addition, there are cellular responses to insulin and IGF stimuli, which ties metabolic signaling to mitochondrial function. The xylan/collagen catabolic and intramembranous ossification terms are less cohesive with this core, possibly reflecting annotation noise or multi-functional proteins, but the primary signal points to mitochondrial energy metabolism coordinated with hormonal signaling.","confidence":"Medium","size":25,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":3},{"id":"GO:0030574","count":2},{"id":"GO:0001957","count":2},{"id":"GO:0046902","count":2},{"id":"GO:0051881","count":2}]},{"hash":"1863910422985627978","title":"Photosynthesis and mitochondrial redox regulation","description":"The terms cluster around energy metabolism and redox control: photosynthesis, mitochondrial electron transport (cytochrome c to oxygen), cytochrome c-heme linkage, hydrogen peroxide metabolism, oxidant detoxification, and redox homeostasis, with links to apoptosis. This suggests a coherent theme of redox balance and energy production across chloroplasts and mitochondria in plant cells, including responses to oxidative stress.","confidence":"High","size":24,"edges":241,"triangles":1574,"max_degree":22,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0055114","count":11},{"id":"GO:0015979","count":6},{"id":"GO:0098869","count":5},{"id":"GO:0045454","count":4},{"id":"GO:0034465","count":4}]},{"hash":"1929438488937381642","title":"Ubiquitin-dependent regulation of cell cycle and cell death","description":"The GO terms cluster around ubiquitin-mediated protein turnover (polyubiquitination, ubiquitin-dependent catabolic process) and cell cycle control (spindle assembly, regulation of cell cycle), as well as cell death pathways (apoptotic and necroptotic processes). While there are additional terms touching on transcription and Toll-like receptor signaling, the dominant theme is ubiquitin-driven regulation of cell cycle progression and cell fate decisions, with some ancillary regulatory roles elsewhere.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":6},{"id":"GO:0051225","count":4},{"id":"GO:0042787","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0071157","count":3}]},{"hash":"1891453183611856197","title":"Ciliary signaling and visual perception","description":"The most represented terms are visual perception and cilium assembly, which point to a set of proteins involved in ciliary function and sensory signaling, particularly in photoreceptor-like contexts. Additional terms for transcription, cell cycle, and GTPase regulation suggest these proteins also participate in broader cellular signaling and regulatory processes that intersect with ciliary pathways. Therefore, labeling this cluster as ciliary signaling with visual perception captures the dominant theme, with secondary roles in general transcriptional and cell-cycle activities.","confidence":"Medium","size":24,"edges":54,"triangles":36,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":10},{"id":"GO:0000278","count":10},{"id":"GO:0033160","count":7},{"id":"GO:0006351","count":7},{"id":"GO:0043547","count":7}]},{"hash":"583279320548698526","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":202,"triangles":945,"max_degree":22,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0048701","count":6},{"id":"GO:0031047","count":6},{"id":"GO:0048026","count":6},{"id":"GO:0019079","count":5}]},{"hash":"1964296233223052935","title":"Bacterial transcriptional regulation and biofilm switch","description":"This cluster centers on bacterial regulatory processes, including regulation of DNA-templated transcription and phosphorelay signaling, together with life-cycle decisions like biofilm formation and flagellum control. The presence of biofilm adhesion, motility regulation, and antibiotic response suggests a cohesive theme of transcriptional control guiding lifestyle switches and stress responses in bacteria, with some metabolic context from glycolysis. Some terms appear less coherent with bacteria (e.g., embryonic neurocranium morphogenesis), indicating possible annotation noise, but the core signal aligns with bacterial transcriptional regulation and biofilm/motility switching.","confidence":"Medium","size":24,"edges":47,"triangles":32,"max_degree":20,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":6},{"id":"GO:0000160","count":5},{"id":"GO:0055114","count":3},{"id":"GO:0043709","count":3},{"id":"GO:1902201","count":3}]},{"hash":"1931040266036030721","title":"Actin Cytoskeleton Remodeling and Protein Localization","description":"This cluster is most characterized by actin filament bundle assembly, cell migration, and maintenance of protein localization at the plasma membrane, all pointing to cytoskeletal dynamics and targeted protein trafficking. Protein ubiquitination also supports regulation of protein turnover linked to these processes. Some terms (e.g., cold response, transcription regulation, cardiac signaling) appear as outliers, but the dominant theme ties to actin-driven rearrangements and localization. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051017","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0016567","count":3},{"id":"GO:0009409","count":3},{"id":"GO:0000122","count":3}]},{"hash":"1759931941549439216","title":"Ubiquitin-mediated control of transcription, signaling, and cell fate","description":"The cluster is enriched for ubiquitination-related processes (polyubiquitination, autoubiquitination, ubiquitin-dependent proteolysis) and regulatory roles across transcription (negative regulation of transcription by RNA polymerase II), signaling pathways (regulation of toll-like receptor signaling, Wnt receptor catabolic process), and cell fate outcomes (cell cycle regulation, necroptosis, apoptosis). This points to a unified theme where ubiquitin-mediated regulation modulates transcription, innate signaling, and cell fate decisions.","confidence":"High","size":24,"edges":26,"triangles":0,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:0071157","count":4},{"id":"GO:0034121","count":4},{"id":"GO:0043066","count":4},{"id":"GO:0000209","count":4}]},{"hash":"13204512206515421","title":"Unknown","description":"Top terms cover microtubule-based transport, spliceosomal assembly, and various developmental processes (hair follicle maturation, nervous system and spermatid development), plus lifespan regulation. These diverse functions do not converge on a single clear theme, making a cohesive label unlikely. ","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043087","count":2},{"id":"GO:0048820","count":2},{"id":"GO:0000387","count":1},{"id":"GO:0000245","count":1},{"id":"GO:0019060","count":1}]},{"hash":"647548593751791984","title":"Diverse solute transporters","description":"The top GO terms indicate multiple transmembrane transport activities for a range of substrates (nitrate, nitrite, arabinose, glucose, urate, trehalose, dehydroascorbic acid, sodium ions, etc.), suggesting these proteins broadly function as membrane transporters rather than a single substrate pathway. Despite no reported edges, the functional signal is transport across membranes for diverse solutes. ","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":2},{"id":"GO:1904728","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0044381","count":2},{"id":"GO:0015747","count":2}]},{"hash":"101355274378110521","title":"Amino acid transport across cell membranes","description":"The top GO terms are centered on importing specific amino acids (D-aspartate, L-glutamate, serine, threonine) and general transmembrane transport, indicating a core function in amino acid movement across membranes. Some terms related to chloroplast/mitochondrial RNA processing and respiration are present but do not define the primary theme of this cluster, suggesting possible ancillary roles or annotation noise. Thus, the label captures the most coherent and frequent function among the proteins: amino acid transport across membranes.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070779","count":1},{"id":"GO:0051938","count":1},{"id":"GO:0055085","count":1},{"id":"GO:0032329","count":1},{"id":"GO:0009449","count":1}]},{"hash":"2298680693616004975","title":"Innate immune signaling and antigen presentation","description":"This cluster is dominated by GO terms related to innate immune sensing and activation (NLRP3 inflammasome assembly, TLR9 signaling, NF-\u03baB pathways, interferon-beta production), plus modules for antigen processing and presentation (MHC class I biosynthesis, dendritic cell antigen presentation) and autophagy/xenophagy. Together, they point to a cohesive functional module coordinating pathogen recognition, inflammatory signaling, and antigen presentation to T cells.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044546","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0034162","count":2},{"id":"GO:0045359","count":2},{"id":"GO:0046827","count":2}]},{"hash":"161456744793736719","title":"Chromatin remodeling and genome maintenance","description":"This cluster is enriched for processes tied to chromatin state and genome integrity: rDNA heterochromatin formation, nucleosome density regulation, transcriptional repression by RNA Pol II, chromatin remodeling, and DNA methylation-related regulation, plus base-excision and replication-associated double-strand break repair. While a few terms (cobalamin biosynthesis, response to light, rRNA methylation) are peripheral, the dominant theme ties chromatin dynamics to transcription control and genome maintenance.","confidence":"Medium","size":24,"edges":115,"triangles":257,"max_degree":21,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000183","count":7},{"id":"GO:0060303","count":7},{"id":"GO:0000122","count":7},{"id":"GO:0009236","count":6},{"id":"GO:0009416","count":6}]},{"hash":"1062976327873555841","title":"DNA replication and mitotic chromosome dynamics","description":"The top terms point to core processes of DNA replication, spindle assembly, and chromatin remodeling, with regulation of sister chromatid cohesion and mitotic chromosome maintenance. Ubiquitination and post-translational targeting hint at coordinated protein turnover and trafficking during the cell cycle, supporting a cohesive theme of replication coupled with chromosome segregation and chromatin state control.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0000209","count":3},{"id":"GO:1904908","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0043044","count":2}]},{"hash":"1421680963112375474","title":"Embryonic organogenesis and neural crest development","description":"The GO terms center on developmental and morphogenetic processes across several tissues (glial proliferation, neural crest cell migration, endocrine pancreas development, embryonic digestive tract morphogenesis, and ureteric bud branching morphogenesis). additively, regulation of transcription and translation and mRNA decay points to coordinated gene expression control during development. The shared theme appears to be embryonic morphogenesis with neural development.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014009","count":2},{"id":"GO:1902042","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0031018","count":2},{"id":"GO:0090190","count":2}]},{"hash":"573939051083798427","title":"Glutamatergic synapse regulation and trafficking","description":"The top GO terms cluster around neuronal synaptic activity, especially glutamatergic transmission and long-term potentiation, plus receptor recycling and regulation of endosome size, indicating vesicle trafficking and synaptic plasticity. Rho signaling linkage suggests cytoskeletal remodeling at synapses, supporting a cohesive theme of synaptic signaling and receptor trafficking rather than unrelated processes.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0016525","count":2},{"id":"GO:0001881","count":1},{"id":"GO:0051036","count":1}]},{"hash":"1139821585943177321","title":"Neural development and behavior","description":"The Top Terms include CNS morphogenesis, behavioral response to ethanol, fear response, and righting reflex, which together point toward neural development and behavioral functions. Additional terms such as regulation of transcription and spliceosomal complex assembly suggest broader gene-expression control, while the ERAD-related term hints at protein quality control that can be relevant in neurons. Overall, the cluster appears to reflect neural development and behavioral function rather than a single enzymatic pathway, though some terms may be incidental annotations.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035520","count":1},{"id":"GO:1904378","count":1},{"id":"GO:1900425","count":1},{"id":"GO:0048149","count":1},{"id":"GO:0001662","count":1}]},{"hash":"1764395435708548230","title":"ER Stress and Protein Folding","description":"The cluster is enriched for endoplasmic reticulum\u2013related functions, notably protein folding in the ER and responses to ER stress, together with oxidative stress detoxification and redox processes. This points to a coordinated ER quality-control/stress response program that handles protein maturation and cellular redox balance; a small subset of terms also hints at regulation of nuclear transport and transcription, but the dominant theme is ER folding and stress.","confidence":"High","size":24,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0033158","count":2},{"id":"GO:0034599","count":2},{"id":"GO:0018401","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2}]},{"hash":"1240888572000164118","title":"Transmembrane Ion and Nutrient Transporters","description":"The top GO terms point to a broad set of transmembrane transport activities: ion transport (Na+, K+, phosphate, nitrate), vitamin and xenobiotic transport, and related substrate movement, including neurotransmitter loading into synaptic vesicles. This coherence suggests a cluster of membrane transporter proteins with diverse but shared transport roles.","confidence":"High","size":24,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":9},{"id":"GO:0071805","count":9},{"id":"GO:0006855","count":9},{"id":"GO:0042891","count":9},{"id":"GO:1900754","count":8}]},{"hash":"15877267570349046","title":"Mitochondrial import and membrane dynamics","description":"This cluster centers on mitochondrial processes: protein insertion into the inner mitochondrial membrane, mitochondrial membrane fission, and unfolded protein response, plus historical terms related to mitochondrial genome maintenance and DNA-templated transcription/DNA replication, which likely reflect nuclear-encoded factors targeting or regulating mitochondria. The inclusion of a glutamatergic synaptic term may reflect mitochondrial roles in neurons rather than a direct functional overlap. Overall, the dominant theme is mitochondria-focused maintenance and dynamics.","confidence":"Medium","size":24,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000002","count":4},{"id":"GO:0034198","count":3},{"id":"GO:0090149","count":3},{"id":"GO:0006355","count":2},{"id":"GO:0045039","count":2}]},{"hash":"1766144302875459336","title":"Bacterial stress response and transport","description":"This cluster aggregates proteins linked to the bacterial SOS and antibiotic response, plus multiple transport-related processes (teichoic acid, bacteriocin, pheromone export, and various ion/vitamin transports) and related assembly/regulatory functions, suggesting a cohesive theme of stress adaptation linked to membrane/transport activities.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009432","count":7},{"id":"GO:0046677","count":6},{"id":"GO:0015777","count":5},{"id":"GO:0043213","count":5},{"id":"GO:0015734","count":5}]},{"hash":"1912793173755485398","title":"Neural-immune Hormonal Signaling","description":"This cluster centers on multiple interconnected signaling pathways: axonogenesis regulation (neural development), GPCR and adenylate cyclase signaling, TLR/MyD88 immune signaling, estrogen receptor signaling, acetylcholine and hormone metabolism, and ovarian follicle growth. The GO terms suggest cross-talk among neural, immune, and hormonal systems rather than a single, cohesive pathway, so a label emphasizing integrated neural-immune-hormonal signaling is most representative.","confidence":"Medium","size":24,"edges":130,"triangles":170,"max_degree":18,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0050770","count":24},{"id":"GO:0032962","count":24},{"id":"GO:0032350","count":24},{"id":"GO:0034158","count":24},{"id":"GO:0007189","count":24}]},{"hash":"2231029489674940847","title":"Membrane Transporters and Osmotic Response","description":"The top GO terms point to multiple membrane transport activities (choline, spermidine, glycine betaine transport; xenobiotic export) and an osmotic stress response, suggesting a cohesive theme around transporter function and osmoregulation. While there are a couple of broader signaling terms, the transport and osmotic-related terms are the most salient, supporting a label focused on membrane transport and osmotic regulation.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033615","count":1},{"id":"GO:0015871","count":1},{"id":"GO:1903711","count":1},{"id":"GO:0046618","count":1},{"id":"GO:0031460","count":1}]},{"hash":"1038827899900839813","title":"Mitochondrial respiration and Fe-S cluster regulation","description":"The cluster\u2019s terms cluster around mitochondrial electron transport (succinate to ubiquinone) and iron-sulfur cluster biology (regulation of Fe-S cluster assembly, response to iron, and cytochrome c release control), with a oxidative stress/response angle (hydrogen peroxide). These together point to mitochondrial respiration and Fe-S cluster regulation as the core theme of the group.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0010722","count":1},{"id":"GO:0006121","count":1},{"id":"GO:0010040","count":1},{"id":"GO:0046621","count":1}]},{"hash":"1193619412563893376","title":"Plant light-regulated gene expression and RNA processing","description":"The dominant GO terms point to plant-specific regulation of gene expression in response to light, including photomorphogenesis and blue light signaling, as well as RNA processing (miRNA processing, RNA methylation, rRNA maturation). A couple of terms are outliers or obsolete (e.g., cannabinoid biosynthesis), but overall the cluster centers on light-regulated transcription and RNA processing in plants.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006349","count":2},{"id":"GO:0051567","count":2},{"id":"GO:0000447","count":2},{"id":"GO:0036265","count":2},{"id":"GO:1901696","count":1}]},{"hash":"312610094903815206","title":"Developmental gene expression and ribosome biogenesis","description":"The cluster centers on core gene-expression and protein-synthesis processes: DNA-templated transcription, mRNA splicing via the spliceosome, ribosome biogenesis (including large subunit biogenesis), and formation of the translation preinitiation complex, with supporting chromatin modification (histone methylation) and protein-trafficking (ER to Golgi). Developmental terms like brain development and multicellular organism growth indicate these processes are tied to developmental programs, suggesting a cohesive role in orchestrating transcription, RNA processing, and ribosome-driven protein synthesis during development.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":9},{"id":"GO:0000398","count":7},{"id":"GO:0035264","count":7},{"id":"GO:0042254","count":7},{"id":"GO:0007584","count":6}]},{"hash":"1289692658186465644","title":"Unknown","description":"The top GO terms span several distinct biological themes: nuclear mRNA export, DNA replication, apoptotic processes, protein oligomerization, peroxisome import, mitochondrial complex III assembly, and plant developmental processes like root hair formation and cell wall organization. This lack of a coherent shared function, along with zero edges, suggests the proteins do not form a single, interpretable functional cluster. Therefore the label is Unknown.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006406","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0080147","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1097806353424701407","title":"Nociception and Inflammatory Signaling","description":"The strongest signals are related to pain perception and nociception (response to pain, detection of mechanical stimulus) together with immune signaling (chemokine/cytokine production, NF-kappaB\u2013related regulation) and cell migration, which together point to inflammatory and nociceptive pathways. An outlier term about cardiac conduction is present but does not alter the overall theme of pain/inflammation. ","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048265","count":11},{"id":"GO:0086070","count":10},{"id":"GO:1903444","count":10},{"id":"GO:0016477","count":10},{"id":"GO:0007253","count":10}]},{"hash":"1067634742088152399","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903265","count":2},{"id":"GO:0061158","count":2},{"id":"GO:0010586","count":2},{"id":"GO:1903886","count":2},{"id":"GO:0035278","count":2}]},{"hash":"1335371444827622643","title":"Redox Metabolism and Growth Regulation","description":"The top GO terms point to redox-related metabolism (oxidation-reduction, redox homeostasis) and thiamine biosynthesis, suggesting a metabolic/redox-focused cluster. A few terms reference regulation of differentiation and stem cell proliferation, but there isn't a strong, cohesive developmental theme across all terms. Thus, a label centered on redox metabolism with a nod to growth regulation best fits, though confidence is low due to mixed signals.","confidence":"Low","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0019383","count":6},{"id":"GO:0045454","count":6},{"id":"GO:0009228","count":6},{"id":"GO:0043046","count":6}]},{"hash":"322125151298536367","title":"TLR signaling and interferon production","description":"Based on the top GO terms, this cluster centers on innate immunity and Toll-like receptor pathways (TLR8/9 signaling, Toll signaling pathway) with regulation of dendritic cell cytokine production and interferon production (IFN-\u03b2 and type II IFN). The dominant signal is pathogen recognition and downstream interferon-mediated responses, despite a couple of unrelated terms that appear as noise. Confidence: High","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0009620","count":4},{"id":"GO:0045359","count":4},{"id":"GO:0034162","count":4},{"id":"GO:0010080","count":4}]},{"hash":"495812455915715234","title":"Carbohydrate Metabolism and Glycolytic Regulation","description":"The prevalence of GO terms tied to fructose metabolism, carbohydrate phosphorylation, and regulation of glucose catabolic flux to lactate via pyruvate suggests a focus on central sugar metabolism. PPP shunt regulation and fructose 2,6-bisphosphate metabolism reinforce a theme of coordinating glycolysis and pentose phosphate pathway activity. While a few terms reference secondary metabolite biosynthesis (arabinan, alkaloids) and cobalamin biosynthesis, these are fewer and do not define the cluster as a single pathway. Overall, the proteins appear anchored to carbohydrate metabolism and its regulatory controls.","confidence":"Medium","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0016311","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0035884","count":2},{"id":"GO:0009820","count":2}]},{"hash":"220287351090858984","title":"Unknown","description":"Unknown","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0036093","count":1},{"id":"GO:0031426","count":1},{"id":"GO:1990180","count":1},{"id":"GO:0072684","count":1}]},{"hash":"845515264551547898","title":"Unknown","description":"The listed GO terms span growth, transcription regulation, TGF-beta signaling, cardiac cell communication, adipocyte differentiation, migration, NF-kappaB regulation, membrane protein localization, macrophage cytokine production, and mechanosensory pain detection. There is no single clear theme connecting these functions, and several terms are unrelated, suggesting a heterogeneous set rather than a cohesive cluster. Confidence in a specific label is therefore None. ","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:2000721","count":2},{"id":"GO:0030511","count":2},{"id":"GO:0086070","count":1},{"id":"GO:1903444","count":1}]},{"hash":"2100502244078321859","title":"Unknown","description":"The top GO terms cover a mix of vertebrate developmental processes (blood vessel branching, mesenchymal and neural/glial development, oligodendrocyte and skeletal muscle development) plus an unrelated bacterial O antigen biosynthetic process and an obsolete hh pathway term. With no cohesive functional theme and no network connectivity, there isn\u2019t a single interpretable function linking these proteins, so a precise label isn\u2019t justifiable.","confidence":"","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009243","count":2},{"id":"GO:0001569","count":1},{"id":"GO:2000729","count":1},{"id":"GO:0002052","count":1},{"id":"GO:0008347","count":1}]},{"hash":"1626786901364123512","title":"Photosynthesis and light-response proteins","description":"Most terms are about photosynthesis and light response: photosynthesis, light harvesting in photosystem II, nonphotochemical quenching, responses to red light and UV-A, and high/low light intensity. A single transcription-related term appears, but the dominant pattern is chloroplast/light-driven energy capture and photoprotection, suggesting the cluster consists of proteins involved in photosynthesis and light signaling.","confidence":"High","size":24,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0071486","count":1},{"id":"GO:0009645","count":1},{"id":"GO:0018298","count":1},{"id":"GO:1904964","count":1}]},{"hash":"913795170698274832","title":"Ubiquitin-Proteasome\u2013Mediated Proteolysis and Signaling","description":"The cluster is dominated by ubiquitin-dependent proteolysis terms (ubiquitin-dependent protein catabolic process, SCF-dependent proteasomal ubiquitination, autoubiquitination) and by terms about regulation of NF-\u03baB (I\u2011\u03baB phosphorylation), JNK signaling, TNF signaling, and apoptosis, suggesting a cohesive theme of ubiquitin\u2011mediated protein turnover and downstream signaling. The X chromosome dosage compensation term appears as a minor outlier.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":10},{"id":"GO:0031146","count":7},{"id":"GO:1903265","count":6},{"id":"GO:0051865","count":6},{"id":"GO:0030433","count":6}]},{"hash":"313835675359985630","title":"Antibiotic and Vitamin K biosynthesis with central metabolism","description":"The cluster is enriched for antibiotic biosynthesis and phylloquinone/menaquinone (Vitamin K) biosynthesis, alongside core metabolic processes like glycolysis, pyruvate production, and fatty acid beta-oxidation. This pattern suggests a cohesive module combining secondary metabolite (antibiotic) biosynthesis with vitamin/cofactor biosynthesis and energy-generating pathways, indicating a broad role in metabolism and biosynthesis.","confidence":"High","size":23,"edges":212,"triangles":1151,"max_degree":22,"top_function":"programmed cell death","top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0006635","count":8},{"id":"GO:0010124","count":7},{"id":"GO:0042372","count":7},{"id":"GO:0006574","count":7}]},{"hash":"846139949410239444","title":"Metabolic Regulation of Differentiation","description":"These proteins are linked to metabolism (thiamine biosynthesis, dihydrolipoamide metabolism) and to differentiation and maturation processes (erythrocyte differentiation, neuron maturation, stem cell proliferation), with additional xenobiotic response signals. The shared theme appears to be metabolic control of developmental processes, justifying the label.","confidence":"Medium","size":23,"edges":36,"triangles":8,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":6},{"id":"GO:0046886","count":4},{"id":"GO:0045648","count":4},{"id":"GO:0009228","count":4},{"id":"GO:0007568","count":4}]},{"hash":"1912225381150927567","title":"Amino acid and vitamin/cofactor biosynthesis","description":"The cluster\u2019s GO terms cluster around biosynthetic and metabolic pathways, especially amino acid biosynthesis/catabolism variants (even though some are obsolete) and the biosynthesis of vitamins and cofactors (biotin, protoporphyrinogen IX), plus related processes like antibiotic biosynthesis and retinol metabolism, suggesting a cohesive theme of cellular biosynthesis and metabolism rather than signaling or response pathways.","confidence":"Medium","size":23,"edges":98,"triangles":194,"max_degree":14,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0019518","count":5},{"id":"GO:0043278","count":4},{"id":"GO:0009097","count":4},{"id":"GO:0006782","count":4}]},{"hash":"437920340365664010","title":"Cardiac signaling and calcium adhesion","description":"The top GO terms point to calcium-related processes (calcium ion concentration in the ER; calcium-dependent cell-cell adhesion) and cardiac-specific signaling and structure (bundle of His/Purkinje cell communication, ectoderm development context with cardiac signaling, and negative regulation of Wnt signaling), along with some broader cellular processes (proton transport, vesicle assembly, promoter binding). Taken together, these suggest a cluster linked to heart development and intercellular signaling mediated by calcium and adhesion, with a broader developmental signaling context.","confidence":"Medium","size":23,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0015991","count":8},{"id":"GO:1904798","count":7},{"id":"GO:0086019","count":7},{"id":"GO:0071255","count":7},{"id":"GO:0032471","count":7}]},{"hash":"141931054656928680","title":"Membrane Transport and Secretion","description":"The cluster is dominated by GO terms related to transport and export across membranes\u2014bacteriocin transport, teichoic acid transport, xenobiotic export, oligopeptide export, taurine transmembrane transport, and ceramide translocation\u2014suggesting a cohesive membrane-transport/secretion theme. Translation and nucleotide-excision repair terms appear but are peripheral to this primary signal.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0046618","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0015910","count":2},{"id":"GO:0015777","count":2}]},{"hash":"1271467953470541711","title":"Root hair cell wall glycoprotein biosynthesis","description":"The cluster centers on plant cell wall biology and secreted glycoproteins. Frequent GO terms include cell wall organization, root hair cell development, arabinogalactan protein metabolism, and rhamnogalacturonan II/pectin biosynthesis, all pointing to glycosylated cell wall components such as arabinogalactan proteins. The glycosylation-related terms (O-linked glycosylation via N-acetyl-galactosamine) further support a theme of plant cell wall glycoproteins driving cell wall assembly and root hair morphogenesis; some terms (e.g., insect visual primordium formation) appear incidental. ","confidence":"High","size":23,"edges":225,"triangles":1270,"max_degree":22,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":7},{"id":"GO:0080147","count":6},{"id":"GO:0016266","count":4},{"id":"GO:0010306","count":3},{"id":"GO:0075015","count":3}]},{"hash":"53292219646373269","title":"Metabolism, redox balance, and xenobiotic response","description":"The terms cluster around core energy metabolism (glycolysis, TCA cycle), redox maintenance (cell redox homeostasis), and responses to xenobiotics, plus various catabolic and secondary metabolism processes (antibiotic biosynthesis, propylene, uracil). This suggests a cohesive group of proteins involved in central metabolism with stress/detoxification roles. High","confidence":"","size":23,"edges":24,"triangles":3,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042208","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0042135","count":3},{"id":"GO:0042420","count":3}]},{"hash":"284269296941767163","title":"NF-kappaB\u2013linked immune signaling","description":"Top GO terms center on NF-kappaB transcription factor activity regulation, NOD2 signaling, and inflammatory mediator production, suggesting a shared role in innate immune signaling and inflammatory responses. Some terms pertain to plant or metabolic processes (leaf senescence, brown fat differentiation) or sensory pain, which appear less directly related and may reflect broader or cross-annotated functions, but the dominant theme is NF-kappaB\u2013driven immune signaling and inflammation.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0070431","count":2},{"id":"GO:1900056","count":1},{"id":"GO:0086070","count":1},{"id":"GO:1903444","count":1}]},{"hash":"604496467224517748","title":"Transcriptional Regulation and Cell Cycle","description":"The cluster shows enrichment for DNA-templated transcription and negative regulation of transcription by RNA polymerase II, along with cell cycle, cell division, and regulation of cell shape, suggesting a core theme of transcriptional control linked to proliferation. Developmental terms (midbrain-hindbrain boundary morphogenesis and fourth ventricle development) also appear, reinforcing a regulatory network context; a couple of bacterial terms (peptidoglycan biosynthetic process, cell wall organization) may be noise or cross-species annotation. Overall, the signal points to transcriptional regulation coupled with cell division and development.","confidence":"Medium","size":23,"edges":11,"triangles":0,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0071555","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0008360","count":2}]},{"hash":"2270609336413686029","title":"Plant chromatin remodeling and telomere regulation","description":"Top terms point to chromatin remodeling, heterochromatin formation at rDNA, and telomere-associated regulatory processes, with supporting links to plant-specific developmental responses. The cluster likely represents nuclear genome organization and maintenance in plants, rather than a single cytoplasmic pathway, hence a label focused on chromatin/telomere regulation fits best.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0043044","count":4},{"id":"GO:0009739","count":3},{"id":"GO:1900033","count":3},{"id":"GO:1990414","count":3},{"id":"GO:1905778","count":3}]},{"hash":"255848203837973621","title":"Spliceosome-driven RNA processing and silencing","description":"The cluster\u2019s top terms largely point to post-transcriptional regulation: multiple spliceosome-related processes (mRNA splicing, alternative splicing regulation), mRNA modification, regulatory ncRNA- and miRNA-mediated silencing, and even translation initiation complex assembly. This suggests a coherent theme of RNA processing and RNA-mediated gene silencing influencing gene expression, with minor developmental association from blastocyst formation not altering the core function.","confidence":"High","size":23,"edges":78,"triangles":97,"max_degree":14,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:1901407","count":11},{"id":"GO:0031047","count":10},{"id":"GO:0048026","count":10},{"id":"GO:0045292","count":8},{"id":"GO:0006378","count":8}]},{"hash":"1259166632805515362","title":"Acetyl-CoA Centered Metabolism and Fatty Acid Biosynthesis","description":"The top GO terms cluster around production of acetyl-CoA via glycolysis and pyruvate decarboxylation, feeding into the TCA cycle and enabling fatty acid biosynthesis (malonyl-CoA and long-chain FA biosynthesis). Lysine and kynurenine catabolic routes also contribute acetyl-CoA\u2013related flux. Notch signaling is present but appears peripheral. Overall, the proteins likely function in central carbon metabolism linked to lipid biosynthesis.","confidence":"High","size":23,"edges":225,"triangles":1381,"max_degree":22,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0033512","count":12},{"id":"GO:2001295","count":8},{"id":"GO:0042759","count":8},{"id":"GO:0019878","count":8},{"id":"GO:0042853","count":7}]},{"hash":"1881819070212987908","title":"Vitamin and Xenobiotic Transmembrane Transporters","description":"The top GO terms are dominated by transmembrane transport activities for vitamins and xenobiotics, including export from the cell and teichoic acid/bacteriocin transport, indicating a cluster of membrane transporter proteins. A few terms related to nucleotide excision repair or DNA replication appear only once and do not define the core function, so the label emphasizes transporter activity.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035461","count":2},{"id":"GO:0006855","count":2},{"id":"GO:0045900","count":1},{"id":"GO:0046618","count":1},{"id":"GO:0006289","count":1}]},{"hash":"1122793559491357481","title":"Innate Immune Signaling and Autophagy Regulation","description":"The cluster is dominated by GO terms linking innate immune sensing and autophagy, notably positive regulation of macroautophagy, TLR8 signaling, and defense response to virus, which together point to an immune-autophagy regulatory module. Additional terms reflect broader signaling pathways (GPCR/cAMP, PLC activation) that can intersect with immune signaling, plus some developmental and homeostatic processes. Overall, the strongest theme is innate immune signaling coupled with autophagy control.","confidence":"Medium","size":23,"edges":212,"triangles":1211,"max_degree":21,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0016239","count":19},{"id":"GO:0034158","count":19},{"id":"GO:0060408","count":19},{"id":"GO:0007190","count":19},{"id":"GO:0007200","count":19}]},{"hash":"366650420807751476","title":"Nuclear RNA Decay and Histone Methylation","description":"The top GO terms point to nuclear RNA turnover (nuclear polyadenylation-dependent rRNA catabolic process and histone mRNA catabolic process) and chromatin-associated modifications (methylation and peptidyl-lysine dimethylation). Although a developmental signal appears (heart/muscle development), the strongest, cohesive theme across the terms is nuclear RNA decay coupled with histone methylation, supporting this label. ","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071035","count":2},{"id":"GO:0071044","count":2},{"id":"GO:0007224","count":2},{"id":"GO:0043642","count":1},{"id":"GO:0032259","count":1}]},{"hash":"762179625844201974","title":"Golgi\u2013endosome trafficking and lipid metabolism","description":"Dominant GO terms indicate Golgi-to-plasma membrane transport and endosome-to-Golgi retrograde transport, suggesting a core Golgi/endosome trafficking function. Lipid metabolism terms (very long-chain and medium-chain fatty-acyl-CoA) add a metabolic context; translation is less central. Overall, this cluster reflects Golgi/endosome trafficking with linked lipid metabolism.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0043001","count":2},{"id":"GO:0042147","count":2},{"id":"GO:0090502","count":2},{"id":"GO:0036111","count":2}]},{"hash":"191319223811045223","title":"Innate Immune Signaling and Inflammasome Activation","description":"The proteins show enrichment for innate immune processes: xenophagy regulation, interferon-beta production, LPS signaling, dsRNA response, TLR9 signaling, and NLRP3 inflammasome assembly, along with ubiquitin-proteasome\u2013dependent protein turnover. This reveals a cohesive theme around pathogen recognition and proinflammatory signaling culminating in inflammasome activity, with autophagy-related involvement. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:1904417","count":4},{"id":"GO:0045359","count":4},{"id":"GO:0031663","count":4},{"id":"GO:0046827","count":4},{"id":"GO:0045087","count":4}]},{"hash":"428066776766232533","title":"Chloroplast Fe-S cluster assembly and RNA processing","description":"Based on the top GO terms, the cluster is enriched for 2Fe-2S/Fe-S cluster assembly and transfer, which are central to chloroplast biogenesis, plus chloroplast/polycistronic RNA processing, indicating roles in organellar RNA metabolism. Some terms reference transcriptional responses to iron, suggesting a broader iron-regulation context. While several terms are obsolete and there is no interaction network, the linking theme around chloroplast Fe-S biogenesis and RNA processing supports this label.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097428","count":1},{"id":"GO:0044571","count":1},{"id":"GO:0034396","count":1},{"id":"GO:0036086","count":1},{"id":"GO:1903026","count":1}]},{"hash":"1907648992124558534","title":"Mitochondrial and chloroplast gene expression","description":"The cluster is dominated by terms related to organelle gene expression and ribosome assembly, including mitochondrial transcription and ribosome assembly, plastid rRNA transcription, and chloroplast organization, suggesting a cohesive theme of mitochondrial/chloroplast gene expression and RNA processing, with a few metabolic terms likely incidental. ","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061668","count":3},{"id":"GO:0042794","count":2},{"id":"GO:0009658","count":2},{"id":"GO:0008380","count":2},{"id":"GO:1903108","count":2}]},{"hash":"62627952360190056","title":"Multisystem Development and Differentiation","description":"Based on the GO terms, the proteins appear enriched for development and differentiation across multiple tissues (neural, bile duct, endocardial, enteric nervous system, skeletal muscle, gland development, etc.). There is no single shared pathway, but a broad theme of tissue-specific developmental processes, suggesting a multisystem developmental role rather than a specific function.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021943","count":2},{"id":"GO:0060807","count":2},{"id":"GO:0048298","count":2},{"id":"GO:0035622","count":2},{"id":"GO:0060956","count":2}]},{"hash":"1681651505875163348","title":"Unknown","description":"The top GO terms cover several disparate areas, including lipid metabolism (triglyceride catabolic process, cholesterol biosynthesis, arachidonate metabolism), membrane trafficking (receptor internalization), and various developmental/signaling processes (neuroblast proliferation, osteoblast development, synapse organization, salicylic acid signaling). Because there isn\u2019t a single, cohesive functional theme tying these terms together, a specific, representative label cannot be confidently assigned.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019433","count":2},{"id":"GO:0015739","count":2},{"id":"GO:0006695","count":1},{"id":"GO:0080151","count":1},{"id":"GO:0051262","count":1}]},{"hash":"358488457735839381","title":"Platelet and leukocyte activation signaling","description":"This cluster centers on activation and signaling in platelets and leukocytes, including positive regulation of platelet activation, leukocyte tethering/rolling, Fc-gamma receptor and C-type lectin receptor signaling, basophil activation, and cytoskeletal remodeling via filopodium assembly with associated arachidonate secretion. These terms collectively suggest an immune activation/adherence network involving platelets and leukocytes, with regulatory cues for NK cell chemotaxis as part of broader immune modulation.","confidence":"Medium","size":23,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010572","count":6},{"id":"GO:0051489","count":5},{"id":"GO:2000502","count":4},{"id":"GO:0038094","count":4},{"id":"GO:0036303","count":4}]},{"hash":"822245607799950788","title":"Amino acid and xenobiotic membrane transporters","description":"GO terms show transmembrane transport of multiple amino acids (proline, lysine, histidine, asparagine, glutamate) and xenobiotics, plus vacuolar import events and starvation-related responses. This points to a cohesive theme of membrane transporters responsible for amino acid/nutrient uptake and allocation, including vacuolar transport, rather than enzymes or signaling factors.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006855","count":3},{"id":"GO:0003094","count":3},{"id":"GO:1901481","count":2},{"id":"GO:0015824","count":2},{"id":"GO:0051365","count":2}]},{"hash":"2026167277356756236","title":"Lipid and pigment catabolism with detox","description":"Most top GO terms describe catabolic processes for lipids (monoacylglycerol, triglyceride, phosphatidylserine) and pigments (chlorophyll) as well as detox responses (response to toxic substance). Some terms relate to lipid-derived signaling (endocannabinoid signaling) and plant-specific metabolism (strigolactone), suggesting a theme around lipid- and pigment turnover and associated detox signaling. An outlier term about mitotic intra-S DNA damage checkpoint signaling reduces cohesion, but the dominant pattern is degradation of lipid/pigment molecules with detox context. Confidence: Medium","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:2000124","count":3},{"id":"GO:0052651","count":3},{"id":"GO:0006660","count":3},{"id":"GO:0015996","count":3}]},{"hash":"572330304573164973","title":"Biosynthesis & RNA Modification Enzymes","description":"This cluster shows enrichment for biosynthetic processes (antibiotic, biotin, cobalamin, chlorophyll) along with RNA and protein methylation activities (mRNA capping, guanine-N7 methylation, N-terminal trimethylation), suggesting a group of enzymes involved in both biosynthesis and biomolecule modifications, despite some detox and nodulation signals.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":9},{"id":"GO:0009102","count":6},{"id":"GO:0098869","count":5},{"id":"GO:0015996","count":5},{"id":"GO:0006370","count":5}]},{"hash":"1756643509667716252","title":"Unknown","description":"The top GO terms cover lipid metabolism (sphingolipid and phosphatidylserine), serine transport, ER-stress\u2013related apoptosis, myelination, virus detection, and some mitotic spindle processes, with no single coherent biological theme linking them. Because there is no clear common function or pathway tying all proteins together, a specific, intuitive label cannot be confidently assigned.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902237","count":1},{"id":"GO:0006665","count":1},{"id":"GO:1904222","count":1},{"id":"GO:0006658","count":1},{"id":"GO:0009597","count":1}]},{"hash":"2303014853095658956","title":"Neurodevelopmental transcription & chromatin remodeling","description":"The cluster is enriched for neural development terms (forebrain development, neural tube closure) along with transcriptional regulation (DNA-templated transcription) and chromatin remodeling, plus protein turnover via SCF-dependent ubiquitin-proteasomal pathways. These collectively point to developmental gene regulation in neurodevelopment, making the label representative. A few immune-related terms appear as minor outliers.","confidence":"High","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006349","count":3},{"id":"GO:0007275","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0043044","count":2}]},{"hash":"1200585574433999707","title":"Plant ion transport and calcium homeostasis","description":"The top GO terms concentrate on ion transport across membranes for several ions (sodium, manganese, potassium, calcium) and Golgi-associated calcium homeostasis, with additional hints of chloroplast-related processes (photosystem II assembly) and plant hormone signaling (auxin-activated pathway). This suggests a cohesive theme around membrane ion transport and Ca2+ regulation in plant cells, possibly linking to chloroplast function and broader cellular signaling. Confidence: Medium","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009734","count":2},{"id":"GO:0098719","count":2},{"id":"GO:0006828","count":2},{"id":"GO:0097623","count":2},{"id":"GO:0098703","count":2}]},{"hash":"2165572933643453258","title":"Muscle and Cardiovascular Development","description":"The cluster\u2019s top GO terms cluster around development of muscle and heart, plus branching in blood vessel morphogenesis, indicating a developmental program for musculoskeletal and cardiovascular tissues. Some terms are unrelated or obsolete, and there are no reported edges among proteins, but the strongest signals point to a muscle/heart/vasculature development theme.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0031591","count":2},{"id":"GO:1903070","count":2},{"id":"GO:0006397","count":2}]},{"hash":"539172918174083587","title":"Unknown","description":"The proteins map to a broad set of processes with little overlap: immune antigen processing, cytoskeletal regulation, RNA and epigenetic modifications, small-molecule biosynthesis, and general stress responses. Because there is no clear shared function or pathway across most of the terms, a specific, representative label is not feasible.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019886","count":2},{"id":"GO:0051016","count":2},{"id":"GO:0006370","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0009102","count":1}]},{"hash":"504430594539865835","title":"Phosphate transport and homeostasis","description":"It includes GO terms focused on phosphate transmembrane transport, intracellular phosphate ion homeostasis, regulation of phosphate transport, and response to phosphate starvation, suggesting a shared theme of phosphate metabolism and transport. Additional terms like glycerophospholipid catabolic process reflect phosphate-containing lipid metabolism; however, unrelated terms (embryonic placenta development, nucleotide-excision repair, cold response) appear less central, likely annotations scattered across proteins.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001892","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0006468","count":2},{"id":"GO:0035435","count":1},{"id":"GO:0030643","count":1}]},{"hash":"1990670796157721360","title":"Cellular stress response and gene regulation","description":"The top GO terms point to responses to xenobiotic and oxidative stress, fatty acids, and apoptosis, with supporting themes of transcription regulation, DNA replication, and protein folding. This suggests a broader module involved in sensing stress, modulating gene expression, and maintaining protein homeostasis, rather than a single cohesive pathway.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":2},{"id":"GO:0006261","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0008631","count":1},{"id":"GO:0017006","count":1}]},{"hash":"551438040811631987","title":"Ubiquitin-regulated immune signaling","description":"The top GO terms center on ubiquitination processes (ubiquitin-dependent protein catabolic process; K33-linked ubiquitination; negative regulation of protein ubiquitination) and immune signaling pathways (B cell receptor signaling, pro-T cell differentiation, regulation of mast cell cytokine production). This combination suggests a shared function in ubiquitin-mediated control of immune signaling rather than a single tissue-specific role, despite some noisy development terms. Confidence: Medium","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0050853","count":4},{"id":"GO:0007519","count":4},{"id":"GO:1990390","count":3},{"id":"GO:0031397","count":3}]},{"hash":"409455057710979937","title":"Neural and mesenchymal development","description":"This cluster centers on developmental processes, with terms for oligodendrocyte development, glial cell migration, neuroblast proliferation, and various mesenchymal/tissue morphogenesis aspects (lung mesenchyme, blood vessel branching, ureter development), suggesting a shared theme of neural and mesenchymal lineage development.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0055072","count":1},{"id":"GO:0030218","count":1},{"id":"GO:0001569","count":1},{"id":"GO:2000729","count":1}]},{"hash":"637450823625600281","title":"Unknown","description":"The top GO terms are diverse and largely non-overlapping (stress response, growth regulation, DNA repair, transcriptional regulation, ncRNA silencing) with several obsolete terms, yielding no clear shared function for the cluster. There isn\u2019t a coherent, representative label that captures these proteins\u2019 common role.","confidence":"","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000587","count":1},{"id":"GO:0071475","count":1},{"id":"GO:0001560","count":1},{"id":"GO:0006471","count":1},{"id":"GO:0003257","count":1}]},{"hash":"2102548768519420416","title":"Lipid catabolism and signaling","description":"The top GO terms are dominated by lipid-related catabolic processes (monoacylglycerol, triglyceride, phosphatidylserine) and regulation of endocannabinoid signaling, indicating a core theme around lipid metabolism and lipid-mediated signaling. Some other terms (chlorophyll catabolic process, antibiotic biosynthetic process) suggest broader or cross-annotated metabolic roles, but the common thread across many terms points to lipid metabolism and signaling pathways.","confidence":"Medium","size":23,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":5},{"id":"GO:0055114","count":5},{"id":"GO:2000124","count":4},{"id":"GO:0052651","count":4},{"id":"GO:0006660","count":4}]},{"hash":"1350368979256865708","title":"Ubiquitin-Proteasome System in Innate Immunity","description":"The cluster centers on ubiquitin-dependent protein degradation and signaling regulation, with multiple terms for autoubiquitination, K48/K63-linked ubiquitination, proteasomal pathways (including SCF and ERAD-related), and innate immune signaling via NF-\u03baB and TNF pathways, indicating a cohesive set of ubiquitination machinery linked to immune response regulation.","confidence":"High","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":"autophagy","top_go_terms":[{"id":"GO:0042787","count":11},{"id":"GO:0051865","count":8},{"id":"GO:0070534","count":8},{"id":"GO:0070936","count":7},{"id":"GO:1903265","count":7}]},{"hash":"539923214592928803","title":"Nuclear RNA processing and DNA replication","description":"This cluster is dominated by GO terms tied to nuclear nucleic acid metabolism: DNA replication and unwinding, nonsense-mediated decay of mRNA, mRNA export from the nucleus, snoRNA release during ribosome biogenesis, and rRNA catabolic processes. Although some terms are obsolete or less directly relevant (and a behavioral term appears), the core theme centers on nuclear RNA processing and DNA replication machinery, justifying a label that highlights these interconnected nuclear processes.","confidence":"Medium","size":22,"edges":189,"triangles":906,"max_degree":21,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006268","count":6},{"id":"GO:0000184","count":6},{"id":"GO:0006260","count":5},{"id":"GO:0009432","count":5},{"id":"GO:0016973","count":4}]},{"hash":"2094530958830608522","title":"Ubiquitin-Dependent Proteostasis","description":"This cluster is dominated by GO terms for ubiquitination (K63-linked ubiquitination, autoubiquitination) and ubiquitin-dependent degradation (ERAD-related), with supporting terms on chaperone-mediated assembly, all pointing to a proteostasis/quality-control role centered on tagging and eliminating misfolded or regulatory proteins. Some other terms (ethanol, chitin, hormone-related) are peripheral and do not outweigh the central ubiquitin/proteostasis theme.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"photosynthesis","top_go_terms":[{"id":"GO:0070534","count":8},{"id":"GO:0051865","count":8},{"id":"GO:0030433","count":8},{"id":"GO:0090035","count":7},{"id":"GO:0071361","count":7}]},{"hash":"632509475222272726","title":"Innate Immune Signaling and Ubiquitination","description":"This cluster is dominated by terms tied to innate immunity (innate immune response, defense against virus) and signaling pathways involving NF-kappaB and NOD2, along with ubiquitin-dependent protein turnover. The repeated emphasis on ubiquitination and transcription factor regulation points to immune signaling modulated by ubiquitin pathways. Some terms reflect broader stress responses (mechanical stimulus) or cell-cycle regulation, but the core theme remains immune signaling with ubiquitin-mediated regulation.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":4},{"id":"GO:0071260","count":4},{"id":"GO:0070431","count":4},{"id":"GO:0000209","count":4},{"id":"GO:0032212","count":3}]},{"hash":"385152048234344536","title":"Developmental transcription and organogenesis","description":"This cluster is dominated by GO terms tied to development across multiple tissues (mesoderm formation, heart development, hippocampus and cerebellar cortex development) and by general transcriptional activity (DNA-templated transcription; regulation of transcription factor activity). Together, they point to proteins involved in developmental regulation and organogenesis, with transcriptional control as a common mechanism. Some outliers (e.g., response to cocaine, antibiotic biosynthetic processes) may reflect broader annotation or multifunctionality but do not override the core theme.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043433","count":2},{"id":"GO:0033138","count":2},{"id":"GO:0042220","count":2},{"id":"GO:0001707","count":2},{"id":"GO:0021766","count":2}]},{"hash":"596220495345632720","title":"Unknown","description":"The GO terms span disparate processes from retinol and fatty acid metabolism to ectoine biosynthesis and a fungal secondary metabolite (verruculogen) biosynthesis, plus an outlier vascular development term; with no clear shared function or interaction pattern connecting the 22 proteins, a coherent, specific label cannot be assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":10},{"id":"GO:0042572","count":5},{"id":"GO:0042264","count":4},{"id":"GO:0042400","count":3},{"id":"GO:0006633","count":3}]},{"hash":"1423889335980387609","title":"Developmental Transcriptional Regulation and Epigenetics","description":"The cluster\u2019s top GO terms center on transcriptional control (DNA-templated transcription; transcriptional regulation) and signaling/differentiation processes (Notch signaling regulation; positive regulation of myoblast differentiation; vasculogenesis). Epigenetic hints appear via histone demethylation terms (even if obsolete), suggesting chromatin-based gene regulation during development. A metabolic term for serine biosynthesis may support differentiation, but the dominant theme ties to developmentally regulated gene expression. Overall, these proteins likely function as transcriptional and epigenetic regulators in developmental contexts.","confidence":"Medium","size":22,"edges":17,"triangles":0,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0006564","count":5},{"id":"GO:2001214","count":5},{"id":"GO:0061428","count":5}]},{"hash":"2180931504350670119","title":"Ubiquitin-Proteasome Mediated Protein Degradation","description":"The cluster is dominated by GO terms related to ubiquitin-dependent protein catabolic processes, including SCF-dependent proteasomal degradation and protein polyubiquitination, indicating a focus on proteostasis via ubiquitin tagging and proteasome breakdown. Supporting terms like cell growth and skeletal muscle cell differentiation suggest that turnover of regulatory proteins may influence muscle development. A few terms tied to NF-kappaB regulation or G1/S transcription appear tangential or obsolete, but do not override the main ubiquitin-proteasome theme. Overall, the functions cohere around controlled protein degradation and its link to growth/differentiation processes.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0000083","count":4},{"id":"GO:0032088","count":3},{"id":"GO:0016049","count":3},{"id":"GO:0071260","count":3}]},{"hash":"2295620627628022980","title":"Protein acetylation and related metabolism","description":"This cluster is dominated by acetylation-related GO terms: N-terminal acetylation, peptidyl-lysine acetylation, spermine acetylation, and propionylation variants, plus several acetyl-CoA\u2013linked metabolic processes (arginine biosynthesis, acetoin and N-acetylglucosamine metabolism, ectoine biosynthesis). The recurring acetylation theme ties these proteins together, with some peripheral metabolic terms likely reflecting broader acetyl-group biology or annotation noise.","confidence":"Medium","size":22,"edges":4,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006526","count":9},{"id":"GO:0009447","count":8},{"id":"GO:0018003","count":8},{"id":"GO:2000025","count":8},{"id":"GO:0006044","count":8}]},{"hash":"788502119727551577","title":"Unknown","description":"Unknown","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016042","count":1},{"id":"GO:0061158","count":1},{"id":"GO:1904582","count":1},{"id":"GO:1904246","count":1},{"id":"GO:1904628","count":1}]},{"hash":"779927966303214155","title":"Chemokine signaling and leukocyte migration","description":"The top GO terms strongly point to immune signaling and chemokine production (positive regulation of macrophage inflammatory protein 1 alpha production; positive regulation of chemokine ligand 5 production) and cell migration, suggesting a cluster centered on inflammatory/immune communication and leukocyte movement. Some terms are obsolete or general (GPCR signaling, membrane localization), but the core theme remains chemokine-mediated immune signaling. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007205","count":6},{"id":"GO:0086070","count":5},{"id":"GO:1903444","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0007253","count":5}]},{"hash":"1218355547488109987","title":"RNA modification and chromatin regulation","description":"The cluster is dominated by GO terms for RNA modification (rRNA methylation, tRNA wobble uridine modification, peptidyl-lysine dimethylation) and Chromatin/Transcription control (rDNA heterochromatin formation, negative regulation of transcription by RNA polymerase II), indicating a cohesive theme around RNA/nucleic acid processing and chromatin-mediated transcription regulation. Some metabolic/biosynthetic terms appear but do not define the main functional theme.","confidence":"Medium","size":22,"edges":204,"triangles":1065,"max_degree":21,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":5},{"id":"GO:0042493","count":5},{"id":"GO:0002098","count":5},{"id":"GO:0000183","count":4},{"id":"GO:0018027","count":4}]},{"hash":"1467373615410297593","title":"Calcium-Dependent Cell-Cell Adhesion in Development","description":"This cluster centers on calcium-dependent cell-cell adhesion (GO:0016339), cell migration (GO:0016477), ectoderm development (GO:0007398), and signaling regulation (e.g., Wnt pathway GO:0090090, calcium-related GO:0032471). These terms together point to a cohesive theme of calcium-mediated adhesion guiding developmental processes and tissue signaling, with some cardiac-conduction related adhesion hints. Confidence: Medium","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904798","count":4},{"id":"GO:0086019","count":4},{"id":"GO:0071255","count":4},{"id":"GO:0032471","count":4},{"id":"GO:0086073","count":4}]},{"hash":"1400530060748811465","title":"Glycan biosynthesis and cell wall assembly","description":"This cluster is dominated by GO terms related to carbohydrate biosynthesis and cell wall components, including mannan, cellulose, hyaluronan, glycogen, and various glycosylation processes, suggesting proteins involved in assembling or modifying glycans and cell-wall structures. Some terms (like angiogenesis) are outliers, but the core pattern points to glycan production and cell envelope biology.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001525","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0016266","count":3},{"id":"GO:0010125","count":2},{"id":"GO:0046354","count":2}]},{"hash":"1395330242626881917","title":"Redox Metabolism and Fe-S Cluster Biosynthesis","description":"The cluster\u2019s top GO terms cluster around oxidation-reduction processes, biosynthesis of redox-active cofactors (menaquinone, pyruvate), and assembly of iron-sulfur ([2Fe-2S] cluster) cofactors. Additional terms like cellular oxidant detoxification and various biosynthetic pathways (phenylacetate, antibiotic, ommochrome) fit within a broad metabolic/cofactor-assembly context. This suggests a cohesive group of proteins involved in redox balance and cofactor biosynthesis, with some peripheral metabolic terms, rather than a single narrowly defined pathway.","confidence":"Medium","size":22,"edges":28,"triangles":0,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0010124","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0098869","count":2}]},{"hash":"749738706673735530","title":"Lipid metabolism and ER-Golgi transport","description":"This cluster is dominated by GO terms tied to lipid metabolism (sphingomyelin catabolic process, lipid A biosynthetic process, positive regulation of isopentenyl diphosphate biosynthesis in the mevalonate pathway) and secretory pathway activity (ER-to-Golgi vesicle transport). While there are a few outlier terms like angiogenesis and xenobiotic response, the strongest shared theme is lipid processing coupled with membrane trafficking, supporting the label. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070940","count":4},{"id":"GO:0001569","count":3},{"id":"GO:0016576","count":3},{"id":"GO:0035690","count":3},{"id":"GO:1900486","count":3}]},{"hash":"1915802846449399380","title":"Capsule and cell wall polysaccharide biosynthesis","description":"The top GO terms point strongly to cell envelope construction and glycan production, including capsule polysaccharide biosynthesis, mycolate-containing cell wall assembly, and UDP-galactose\u2013dependent glycosylation. This suggests the cluster represents proteins involved in building and decorating the cell wall/capsule rather than signaling or intracellular processes. A few unrelated insect development terms appear in the list, but the dominant signal centers on polysaccharide biosynthesis and cell-wall organization.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0045227","count":3},{"id":"GO:0071769","count":3},{"id":"GO:0070592","count":3},{"id":"GO:0052573","count":3}]},{"hash":"1255881979929117392","title":"Chromatin modification and transcriptional regulation in development","description":"Most terms indicate transcriptional control and histone modification (DNA-templated transcription; histone demethylation) with links to developmental signaling (Notch, vasculogenesis) and differentiation (osteoblasts), suggesting a cluster of regulatory proteins involved in gene expression during development; a few annotations (redox links, antibiotic biosynthetic process) may reflect broader metabolic regulation or noise.","confidence":"Medium","size":22,"edges":30,"triangles":4,"max_degree":8,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0017000","count":5},{"id":"GO:0034720","count":4},{"id":"GO:0070544","count":4},{"id":"GO:0006351","count":4}]},{"hash":"589311988149185195","title":"Unknown","description":"The top GO terms span diverse processes: cellular response to glucose stimulus, defense against Gram-positive bacteria, sperm capacitation, regulation of cardiac proliferation, keratinocyte differentiation, various signaling events (peptidyl-serine phosphorylation, Hippo, calcineurin-NFAT), actin cytoskeleton organization, and potassium ion transport. There is no single cohesive functional theme that ties these terms together, suggesting the proteins in this cluster have heterogeneous roles rather than a common pathway or function.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071333","count":9},{"id":"GO:0050830","count":8},{"id":"GO:0048240","count":7},{"id":"GO:0060044","count":7},{"id":"GO:0030216","count":7}]},{"hash":"240094067158858872","title":"Unknown","description":"The GO terms include transport, chromatin modification, ROS biosynthesis, hormonal response, brain development, immune activity, cytoskeletal remodeling, and ion transport, a broad and seemingly unrelated mix that does not point to a single shared function. Therefore a concise, representative label cannot be assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015739","count":3},{"id":"GO:0034720","count":2},{"id":"GO:0050665","count":2},{"id":"GO:0051412","count":2},{"id":"GO:0021762","count":2}]},{"hash":"1514113364583227555","title":"Sterol and sphingolipid metabolism","description":"The Top Terms are strongly oriented toward lipid metabolism, including sphingolipid (MIPC) metabolism, ergosterol biosynthesis, sterol oxidation, and ether lipid metabolism, suggesting a core function in sterol/sphingolipid biosynthesis. Some GO terms like brain development and myelin maintenance may be peripheral annotations or cross-species noise, but the dominant signal points to lipid/sterol pathways. Overall, the cluster appears to represent lipid and sterol metabolism rather than a single neural or immune function.","confidence":"Medium","size":22,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006675","count":3},{"id":"GO:0001949","count":3},{"id":"GO:0032286","count":3},{"id":"GO:0034435","count":2},{"id":"GO:0007420","count":2}]},{"hash":"1919848494093585258","title":"Cardiac calcium signaling and heart morphogenesis","description":"The top GO terms are dominated by cardiac-related functions, including ventricular cardiac muscle tissue morphogenesis, regulation of RyR calcium-release channels, and release of calcium from the sarcoplasmic reticulum, indicating a cohesive role in cardiac calcium handling and heart development. Other terms like axonogenesis and lymph vessel morphogenesis are present but less central, suggesting pleiotropy rather than core function. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070542","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0061179","count":2},{"id":"GO:0014808","count":2},{"id":"GO:0043388","count":2}]},{"hash":"1777879461209172632","title":"Unknown","description":"Terms span metabolism, mitochondrial function, hematopoiesis, stress response, and growth signaling, with no overarching shared function. Thus a single cohesive label cannot be assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006067","count":1},{"id":"GO:0061668","count":1},{"id":"GO:0006695","count":1},{"id":"GO:0030097","count":1},{"id":"GO:0006629","count":1}]},{"hash":"343229241878311607","title":"Unknown","description":"The top GO terms cover a wide range of unrelated processes (Golgi retention, mitophagy/autophagy, root meristem growth, cytokinin signaling, glucocorticoid signaling, pericentriolar material localization, neuroblast polarity), and most terms have only a single representation. This lack of a clear, shared function among the cluster members makes it not possible to assign a specific, coherent label, so the appropriate label is Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045053","count":1},{"id":"GO:1905090","count":1},{"id":"GO:0030242","count":1},{"id":"GO:0010449","count":1},{"id":"GO:0080037","count":1}]},{"hash":"1110820020120473360","title":"Calcium-Driven Signaling and Inflammation","description":"The top terms center on calcium ion transport and broad signaling/inflammatory processes (NF-kappaB regulation, MIP-1 alpha production, and cell migration), with additional hints of mechanosensation and cardiac signaling. This suggests a cohesive theme of calcium-mediated signaling linked to inflammatory and migratory responses, rather than a single, highly specific pathway.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":8},{"id":"GO:0098703","count":8},{"id":"GO:0086070","count":7},{"id":"GO:1903444","count":7},{"id":"GO:0016477","count":7}]},{"hash":"551409406012882253","title":"Organelle RNA processing and respiration","description":"The top GO terms are dominated by chloroplast and mitochondrial RNA processing and energy metabolism (chloroplast rRNA processing, mitochondrial RNA processing, inner mitochondrial membrane organization, mitochondrial large ribosomal subunit assembly, and cellular respiration), indicating a core theme of organelle gene expression and respiration. Some other terms relate to plant development or immune signaling and appear as outliers, suggesting a loose cluster rather than a tightly cohesive module. Confidence: Medium","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009911","count":1},{"id":"GO:0042752","count":1},{"id":"GO:0009742","count":1},{"id":"GO:0050853","count":1},{"id":"GO:0002467","count":1}]},{"hash":"332898969834179116","title":"Plant membrane transport and ABA signaling","description":"The terms cluster around membrane transport processes (potassium ion transmembrane transport, cadmium import into vacuole, ceramide translocation, cytosol to ER transport) and ABA-activated signaling involved in stomatal movement, pointing to plant membrane transport and stress signaling; some outliers (bacteriocin-related terms) likely reflect annotation noise, but the dominant theme is transport across membranes in plant cells.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0060081","count":2},{"id":"GO:1901527","count":2},{"id":"GO:0036249","count":2},{"id":"GO:0043213","count":2}]},{"hash":"466067904013172439","title":"Regulation of intracellular transport and turnover","description":"The cluster centers on regulatory roles across diverse intracellular processes rather than a single enzymatic function, including ribophagy, regulation of nuclear mRNA and tRNA export, vesicle-mediated cholesterol transport, phagocytosis, apoptotic control, and modulation of synaptic plasticity and lipid signaling. This pattern suggests a general regulatory/trafficking turnover theme rather than a specific catalytic activity.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034517","count":1},{"id":"GO:0060291","count":1},{"id":"GO:0031914","count":1},{"id":"GO:0060304","count":1},{"id":"GO:0032443","count":1}]},{"hash":"1087316713831649812","title":"DNA-Templated Transcription and Repair","description":"The cluster is dominated by GO terms for DNA-templated transcription and its regulation, plus transcription-coupled nucleotide-excision repair, pointing to a core role in transcriptional control and genome maintenance. Additional terms related to protein folding/processing and stress responses likely reflect ancillary cellular stress handling, but the main theme ties to transcription and DNA repair.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0050832","count":1},{"id":"GO:0009411","count":1},{"id":"GO:0006283","count":1}]},{"hash":"1812331468543765668","title":"Unknown","description":"The GO terms are varied (lipoteichoic acid biosynthesis, IPP biosynthesis, various nucleotide and RNA-related catabolic processes, and even DNA repair and RNA editing), with no clear single function tying all 22 proteins together, so a cohesive cluster label cannot be assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0070395","count":2},{"id":"GO:0009240","count":1},{"id":"GO:1901907","count":1},{"id":"GO:2000781","count":1}]},{"hash":"1240463391255945828","title":"Golgi UDP-sugar transporters","description":"The top GO terms point to transport of nucleotide sugars into the Golgi lumen (UDP-galactose, UDP-N-acetylglucosamine) and related sugar transport (sialic acid), which are foundational for glycosylation and cell-wall/exine formation processes in plants; a few terms about development appear incidental, but the core signal is nucleotide-sugar transport into the Golgi. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001825","count":1},{"id":"GO:0000028","count":1},{"id":"GO:0042840","count":1},{"id":"GO:0097624","count":1},{"id":"GO:1990569","count":1}]},{"hash":"1251584382792986574","title":"Stress-Responsive Signaling and Ubiquitination","description":"This cluster centers on regulatory signaling and stress response processes: several terms point to modulation of signaling pathways (negative regulation of kinase activity, IL-12 production, NF-kB-related processes), ubiquitination, and broader cellular stress responses (cell growth, migration, apoptosis, heat response). The recurring themes suggest proteins that act as regulators of signaling and immune/inflammatory responses, often via ubiquitin-mediated mechanisms and stress signals.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0016477","count":6},{"id":"GO:0007253","count":6},{"id":"GO:0097284","count":6},{"id":"GO:0016049","count":6},{"id":"GO:0050968","count":6}]},{"hash":"1956533385019574299","title":"Chemokine Production and Macrophage Signaling","description":"The top GO terms point to chemokine production and macrophage inflammatory signaling (positive regulation of CCL5 production and MIP-1\u03b1 production), supported by related terms about cell migration and immune-related responses. While some terms are broad or unrelated (e.g., mechanosensation, metabolic differentiation), the core theme centers on chemokine-mediated immune activity and macrophage signaling.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":6},{"id":"GO:0086070","count":5},{"id":"GO:1903444","count":5},{"id":"GO:0016477","count":5},{"id":"GO:0007253","count":5}]},{"hash":"2179728929391265286","title":"TLR signaling and innate immune activation","description":"The cluster is enriched for GO terms related to toll-like receptor signaling (TLR4, TLR9, TLR10) with both MyD88-dependent and -independent pathways, macrophage activation, dendritic cell cytokine production, IL-18 and interferon-beta production, and inflammatory response. Collectively, these terms point to proteins functioning in innate immune sensing and cytokine-mediated inflammation, justifying a label around TLR signaling and innate immune activation.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034162","count":2},{"id":"GO:0045359","count":2},{"id":"GO:0002730","count":2},{"id":"GO:0032741","count":2},{"id":"GO:0042116","count":2}]},{"hash":"2208528035366883203","title":"Developmental Differentiation and ECM Biosynthesis","description":"Top GO terms suggest involvement in tissue development (skeletal muscle differentiation, forebrain development, multicellular organism development) and extracellular matrix formation (chondroitin sulfate proteoglycan biosynthesis). Together they point to a cluster of proteins tied to development and ECM production, with additional associations to ubiquitination and circadian regulation as secondary signals.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0035914","count":2},{"id":"GO:0050650","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0000209","count":2}]},{"hash":"964535283172363159","title":"Unknown","description":"The top GO terms span reproductive development (male sex differentiation, prostate gland development), immune responses (type I interferon signaling, neutrophil regulation), and basic metabolism (glycolysis, fructose response), plus nematode-specific processes. There is no coherent single theme tying these terms together, so Unknown.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046661","count":2},{"id":"GO:0071357","count":2},{"id":"GO:0006463","count":2},{"id":"GO:0030850","count":2},{"id":"GO:0018996","count":1}]},{"hash":"865613664123255011","title":"Glycan Biosynthesis and Glycosylation","description":"The top GO terms are dominated by glycan-related processes: oligosaccharide metabolic process, N-glycan processing, N-linked glycosylation via asparagine, glycosylceramide metabolism, protein sialylation, and ganglioside biosynthesis. These point to a cohesive theme of glycan assembly and modification in proteins and lipids. A few pollen-related terms appear but do not outweigh the central glycosylation signal. Confidence: Medium","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009311","count":1},{"id":"GO:0021628","count":1},{"id":"GO:0006677","count":1},{"id":"GO:1990743","count":1},{"id":"GO:0009860","count":1}]},{"hash":"207371142003746168","title":"Cell cycle and cytoskeleton organization","description":"The cluster shows enrichment for DNA-templated transcription and cell cycle/cell division terms, alongside actin filament bundle assembly and regulation of cell shape, indicating a combined role in cell proliferation and cytoskeletal remodeling. Some metabolic/obsolete terms are present but do not define the core function. ","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0006209","count":2},{"id":"GO:0019556","count":2}]},{"hash":"1631096923654306695","title":"Transcription Regulation & DNA Binding","description":"The top GO terms are dominated by transcriptional regulation and DNA binding (positive/negative regulation of transcription by RNA polymerase II, regulation of DNA binding, and related processes), suggesting these proteins are nuclear transcription regulators. Additional terms like thyroid hormone metabolism and DNA replication support roles in gene expression control and associated cellular processes. Overall, the cluster appears cohesive around transcriptional regulation rather than unrelated functions.","confidence":"High","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000678","count":3},{"id":"GO:0042403","count":3},{"id":"GO:0060316","count":3},{"id":"GO:0043388","count":3},{"id":"GO:0061587","count":2}]},{"hash":"2010033450606591066","title":"Unknown","description":"The Top Terms are highly diverse across signaling, plant hormone response, transcription, DNA repair, viral process, and chromatin organization, with no shared biological function or pathway linking most proteins. The cluster has no edges or cohesive function, so a concise, representative label cannot be assigned.","confidence":"","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0035249","count":2},{"id":"GO:0009739","count":2},{"id":"GO:1900033","count":2},{"id":"GO:1990414","count":2}]},{"hash":"1508115260236768734","title":"Oxidative stress response and proteostasis","description":"These proteins show enrichment for stress-related processes, notably cellular response to hydrogen peroxide (oxidative stress) and proteostasis-related terms such as unfolded protein response and protein quality control via ubiquitination. The presence of K11-linked ubiquitination supports targeted degradation under stress, aligning with a coherent theme of managing oxidative damage and maintaining protein homeostasis. Confidence: Medium","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":3},{"id":"GO:0051348","count":2},{"id":"GO:0016576","count":2},{"id":"GO:1903071","count":2},{"id":"GO:0043278","count":2}]},{"hash":"1381547731498547195","title":"Mitochondrial lipid biosynthesis and energy metabolism","description":"This cluster is driven by several mitochondrial-related terms: mitochondrial ribosome assembly and mitochondrial ATP synthesis coupled electron transport point to core mitochondrial function, while cardiolipin remodeling, ether lipid biosynthesis, triglyceride biosynthesis, and phosphatidylcholine regulation highlight lipid biosynthesis and remodeling happening in mitochondria. Ethanol metabolism can connect to mitochondrial oxidative processes, reinforcing the mitochondrial-centric theme. A few terms like cerebellum morphogenesis, glandular epithelial cell maturation, and cutin biosynthesis may reflect broader or cross-species annotations, but the dominant signal is mitochondrial lipid metabolism and energy production.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006067","count":2},{"id":"GO:0061668","count":2},{"id":"GO:0021587","count":1},{"id":"GO:0042775","count":1},{"id":"GO:0019432","count":1}]},{"hash":"1210478297501443665","title":"Intracellular Protein Transport","description":"The strongest shared annotations are GO:0006605 (protein targeting), GO:0043952 (protein transport by the Sec complex), GO:0017038 (protein import), and GO:0065002 (intracellular protein transmembrane transport), pointing to a common theme of protein trafficking/localization within cells. A few outlier terms (transcription, repair, molting) likely reflect annotation noise or multi-function proteins.","confidence":"Medium","size":22,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006605","count":1},{"id":"GO:0043952","count":1},{"id":"GO:0017038","count":1},{"id":"GO:0065002","count":1},{"id":"GO:0070084","count":1}]},{"hash":"1607396508547533431","title":"Protein ubiquitination and sumoylation regulation","description":"This cluster is dominated by post-translational modification and protein quality-control processes, with strong signals for SUMOylation (GO:0016925), deubiquitination (GO:0016579), and autoubiquitination (GO:0051865), as well as ERAD-related concepts. While there are a few outliers (ribosome subunit assembly, spindle pole body duplication, erythrocyte differentiation), the shared theme is proteostasis and ubiquitin/SUMO pathways, suggesting a cohesive function in protein modification and turnover.","confidence":"Medium","size":21,"edges":168,"triangles":830,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0016925","count":12},{"id":"GO:0016579","count":10},{"id":"GO:0014070","count":9},{"id":"GO:0010637","count":8},{"id":"GO:1904378","count":8}]},{"hash":"608532783908478123","title":"Translational control and ubiquitin-mediated regulation","description":"The cluster is dominated by translation-related terms (translation, 7-methylguanosine mRNA capping) alongside ubiquitination-related processes (K63-linked ubiquitination, autoubiquitination) and cell cycle regulators (negative regulation of CDK activity, cell cycle). This suggests a cohesive theme around protein synthesis and its regulation, including protein folding/quality control via chaperones and turnover via ubiquitin signaling, particularly in cell-cycle or stress contexts.","confidence":"Medium","size":21,"edges":16,"triangles":11,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0006370","count":3},{"id":"GO:0044387","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0045736","count":3}]},{"hash":"1160741764358856377","title":"Diverse Biosynthesis and Metabolic Pathways","description":"This cluster centers on various biosynthetic and metabolic processes (lipid biosynthesis, gluconeogenesis, polymer biosynthesis, antibiotic biosynthesis) with additional plant hormone biosynthesis/signaling and sporulation terms, suggesting a general theme of metabolic and biosynthetic activity rather than a single specific pathway. The diversity and presence of obsolete terms reduce precision, so a cautious, intermediate label is appropriate.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:0046854","count":4},{"id":"GO:0006094","count":4},{"id":"GO:0045453","count":3},{"id":"GO:0042619","count":3}]},{"hash":"1130196728578748768","title":"Redox homeostasis and oxidative stress response","description":"The cluster is dominated by GO terms for oxidation-reduction processes, cellular redox balance, and detoxification of oxidants, along with redox-linked post-translational modifications like deglutathionylation and deubiquitination. These collectively point to a coherent theme of redox regulation of cellular function, with a few peripheral terms reflecting broader metabolic or developmental connections. Confidence: High","confidence":"","size":21,"edges":64,"triangles":118,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0045454","count":5},{"id":"GO:0098869","count":4},{"id":"GO:0016579","count":3},{"id":"GO:0034599","count":3}]},{"hash":"907869496418331967","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":176,"triangles":833,"max_degree":20,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000398","count":16},{"id":"GO:0009432","count":16},{"id":"GO:0071035","count":15},{"id":"GO:0006306","count":15},{"id":"GO:0071051","count":15}]},{"hash":"319416231143221229","title":"ERAD and ER Stress Response","description":"Proteins cluster around ER-associated degradation (ERAD) and ubiquitin-dependent proteolysis, plus ER stress signaling and related proteostasis processes (sumoylation, autophagosome maturation regulation). A few terms for DNA maintenance appear incidental, so the dominant theme is ER proteostasis and stress-induced degradation.","confidence":"Medium","size":21,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1904378","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0000722","count":3},{"id":"GO:0016925","count":3},{"id":"GO:1901340","count":2}]},{"hash":"2118794086040245823","title":"NOD2-Driven Innate Immune Signaling","description":"The cluster is enriched for innate immune and antiviral defense terms, notably the NOD2 signaling pathway and innate immune response, suggesting a core function in pattern-recognition\u2013driven immunity and NF-kappaB\u2013related signaling. Ubiquitination and ubiquitin-dependent protein catabolic processes support regulation of immune signaling cascades. Some telomere- and vitamin D\u2013related terms may reflect broader regulatory roles or pleiotropy, but the dominant theme is NOD2-mediated innate immune sensing and antiviral defense.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0032088","count":7},{"id":"GO:0070431","count":7},{"id":"GO:0045087","count":7},{"id":"GO:0051607","count":7},{"id":"GO:0070198","count":5}]},{"hash":"1755944185798773142","title":"Nucleolar transcription and chromatin regulation","description":"The cluster\u2019s top GO terms center on ribosomal large subunit biogenesis, pointing to nucleolar ribosome assembly, while additional terms describe chromatin state and transcription regulation (histone modification regulation, nucleosome dynamics, RNA Pol II start-site selection, and RNA Pol I transcription termination). This suggests a cohesive theme around nucleolar transcription coupled with chromatin regulation and genome maintenance, despite some obsolete annotations. ","confidence":"Medium","size":21,"edges":10,"triangles":0,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0042273","count":9},{"id":"GO:0071441","count":8},{"id":"GO:0001178","count":8},{"id":"GO:0071894","count":8},{"id":"GO:0042766","count":8}]},{"hash":"178969440667173412","title":"Intracellular Signaling and Trafficking","description":"The top GO terms point to signal transduction regulation (Rap), ion channel activity modulation, plus-end vesicle transport, and cytoskeletal/adhesion aspects, with additional RNA localization and Purkinje cell structure terms. This mix centers on intracellular signaling and trafficking processes rather than a single specialized function, so a general label of intracellular signaling and trafficking fits best.","confidence":"Medium","size":21,"edges":199,"triangles":1148,"max_degree":20,"top_function":null,"top_go_terms":[{"id":"GO:0045190","count":6},{"id":"GO:0032487","count":6},{"id":"GO:0090419","count":6},{"id":"GO:0033624","count":6},{"id":"GO:0072383","count":6}]},{"hash":"849211066414155410","title":"Developmental transcription factors","description":"This cluster\u2019s top GO terms are dominated by DNA-templated transcription and broad developmental processes across multiple tissues (forebrain, cerebellum, heart, skeletal muscle, placenta, visual perception). This pattern suggests proteins involved in coordinating developmental programs through transcriptional regulation, spanning several organ systems rather than a single tissue. The label \u201cDevelopmental transcription factors\u201d captures this shared function without overfitting to a specific tissue.","confidence":"Medium","size":21,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0001890","count":4},{"id":"GO:0021549","count":4},{"id":"GO:0007601","count":4},{"id":"GO:0071375","count":4}]},{"hash":"344050749990286724","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":132,"triangles":412,"max_degree":20,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":15},{"id":"GO:0007601","count":15},{"id":"GO:0043547","count":14},{"id":"GO:0060271","count":13},{"id":"GO:0050709","count":13}]},{"hash":"899982407765740757","title":"Unknown","description":"The top GO terms are highly diverse and include metabolic processes (glutamine and sterol biosynthesis), bacterial biosynthesis (lipopolysaccharide), histone modification, cell cycle, cytolysis, and even vasculogenesis, with several obsolete terms present. This lack of a single cohesive function or pathway across the cluster makes it difficult to assign a specific, representative label, so Unknown is most appropriate.","confidence":"","size":21,"edges":43,"triangles":31,"max_degree":15,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0006541","count":5},{"id":"GO:0009103","count":4},{"id":"GO:0042264","count":4},{"id":"GO:0034720","count":4}]},{"hash":"1834358114055161611","title":"Ubiquitin-Dependent Protein Quality Control","description":"The cluster is enriched for ubiquitin-related processes\u2014K63-linked ubiquitination, autoubiquitination, and ubiquitin-dependent ERAD\u2014along with chaperone-mediated protein complex assembly, indicating a focus on protein quality control via ubiquitin signaling. Additional terms for ethanol and cadmium stress, plus innate immune response, suggest this quality-control machinery is engaged across diverse stress and defense contexts. Overall, the theme centers on ubiquitin-mediated protein quality control during cellular stress.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071361","count":7},{"id":"GO:0045087","count":7},{"id":"GO:0000278","count":6},{"id":"GO:0071276","count":6},{"id":"GO:0030433","count":5}]},{"hash":"586876318265864887","title":"Cardiac development and chromatin remodeling","description":"Proteins in this cluster are enriched for cardiac-related processes: heart development and cardiac muscle contraction, along with negative regulation of skeletal muscle differentiation. The strong presence of chromatin remodeling and DNA-binding regulation terms suggests that these proteins participate in transcriptional control guiding cardiac differentiation, with chromatin dynamics playing a key role. A few cell-cycle related terms (DNA replication, chromosome separation) are present but seem less central, indicating the dominant theme is heart muscle development and transcriptional regulation.","confidence":"Medium","size":21,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2001015","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0060048","count":2},{"id":"GO:0007205","count":2}]},{"hash":"2229011910627835847","title":"Heat stress response and ER protein folding","description":"These proteins show a strong enrichment for heat-related and ER protein quality-control terms: response to heat, unfolded protein response, and protein folding in the endoplasmic reticulum. There are also transcription-related terms, likely reflecting broader stress-induced transcriptional changes, and some translation/assembly terms. Overall, the cluster appears to represent a heat/ER stress response module centered on maintaining protein homeostasis under stress, with some ancillary nuclear transcription signals.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006351","count":3},{"id":"GO:0009408","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1900035","count":3}]},{"hash":"27562998263970524","title":"ER Stress Response and Protein Quality Control","description":"This cluster is enriched for endoplasmic reticulum\u2013related proteostasis terms: unfolded protein response, ER protein folding, and ER-associated degradation, along with translation initiation regulation under ER stress and heat response signals. The combination suggests a cohesive theme of maintaining ER protein homeostasis under stress, with optional links to cell cycle regulation under adverse conditions. Overall, the dominant signal points to ER stress response and proteostasis.","confidence":"High","size":21,"edges":29,"triangles":1,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0006986","count":3},{"id":"GO:0036494","count":3},{"id":"GO:0071157","count":2}]},{"hash":"63130426531672118","title":"Unknown","description":"The terms span cardiac signaling, adipocyte differentiation, plant hormone signaling, transcriptional regulation, and immune-related processes, with many obsolete GO entries and no shared pathway or functional theme, plus no interactions observed, so there is no coherent label to assign.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043046","count":2},{"id":"GO:0086070","count":1},{"id":"GO:0045444","count":1},{"id":"GO:0061408","count":1},{"id":"GO:2000031","count":1}]},{"hash":"366102132410928594","title":"Ciliary development and photoreceptor maintenance","description":"The cluster is dominated by GO terms linked to cilia (motile cilium assembly, intraciliary transport), developmental processes (left-right patterning, neural tube closure, heart looping) and eye/photoreceptor development and maintenance, all pointing to a cilium-centered developmental module that includes photoreceptor function.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060972","count":1},{"id":"GO:0044458","count":1},{"id":"GO:0045494","count":1},{"id":"GO:0001947","count":1},{"id":"GO:0007224","count":1}]},{"hash":"2250549767834252855","title":"Nuclear transcriptional regulation and development","description":"Based on the top GO terms, the cluster is centered on DNA-templated transcription (GO:0006351) and multicellular development (GO:0007275), with several nuclear-localized transcription regulatory processes implied by maintenance of protein location in the nucleus and negative regulation of transcription initiation. Even though some terms are labeled obsolete, the recurring theme is transcriptional regulation within the nucleus tied to developmental processes.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0006349","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0035948","count":2}]},{"hash":"569356875843793527","title":"Developmental signaling and tissue morphogenesis","description":"The prevalent GO terms cluster around signaling pathways (Wnt, Hippo) that govern growth, differentiation, and apoptosis, plus processes of cell migration, DNA replication/transcription, keratinocyte differentiation, and organ/tissue development (lung mesenchyme). This combination suggests a module involved in developmental regulation and tissue morphogenesis.","confidence":"Medium","size":21,"edges":121,"triangles":283,"max_degree":15,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0060044","count":19},{"id":"GO:0030216","count":19},{"id":"GO:0090263","count":19},{"id":"GO:0035329","count":19},{"id":"GO:0006915","count":19}]},{"hash":"1238071171735691787","title":"Antibiotic and fatty acid biosynthesis","description":"The top GO terms are strongly about biosynthetic processes, especially antibiotic biosynthesis (GO:0017000) and clavulanic acid biosynthesis (GO:0033050), plus fatty acid biosynthesis (GO:0006633) and related metabolite biosynthesis (e.g., carnitine biosynthesis). While there are a few other processes (transcription, cell division, some catabolic/oxidation-reduction terms), the dominant signal across the terms indicates a cluster centered on production of small molecules and lipids, particularly antibiotics and fatty acids. Confidence: High","confidence":"","size":21,"edges":33,"triangles":4,"max_degree":6,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0006351","count":4},{"id":"GO:0033050","count":4},{"id":"GO:0046300","count":4},{"id":"GO:0006151","count":4}]},{"hash":"1644845508970834512","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0006351","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0006189","count":3},{"id":"GO:0017000","count":2}]},{"hash":"1738853347766406783","title":"Neuronal development and vesicle trafficking","description":"This cluster centers on neuronal biology, with strong hints from brain development, neurotransmitter transport, ER-to-Golgi vesicle transport, and calcium-dependent exocytosis \u2014 all characteristic of neuronal maturation and secretory pathways. Protein ubiquitination and homooligomerization suggest post-translational regulation and assembly of protein complexes, which can accompany neuronal differentiation and synaptic machinery. Some terms like mitotic spindle assembly and cell division are more general and may reflect shared cellular processes, but the dominant themes point to neuronal development combined with vesicle trafficking and exocytosis.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0007420","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006836","count":2}]},{"hash":"161332888073596817","title":"Nucleic acid repair and RNA processing","description":"The top GO terms cluster around nucleic acid metabolism and genome maintenance (DNA repair, nucleotide-excision repair, deadenylation-dependent mRNA decapping, and exonucleolytic RNA processing). While other terms show broader metabolism and transport, the strongest shared theme among the proteins appears to be nucleic acid processing and repair. This label captures the central signal without overreaching into unrelated processes.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090503","count":2},{"id":"GO:0050992","count":2},{"id":"GO:0000290","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0015967","count":2}]},{"hash":"273708163261652207","title":"Glycolysis and Carbohydrate Metabolism","description":"The cluster's GO terms predominantly describe glycolytic processes and fructose/ carbohydrate metabolism, including glycolysis, fructose metabolism, carbohydrate phosphorylation, and regulation of the PPP shunt and flux toward lactate, with serine biosynthesis also linked to glycolytic intermediates. This suggests a cohesive function in central carbon metabolism, while a single term on tRNA modification appears as noise.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002943","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0006000","count":1},{"id":"GO:0046835","count":1},{"id":"GO:0043456","count":1}]},{"hash":"1592035494661305540","title":"Unknown","description":"Unknown","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0000961","count":2},{"id":"GO:0009793","count":2},{"id":"GO:0080156","count":2},{"id":"GO:0016554","count":2}]},{"hash":"1941136554150032293","title":"Transmembrane transport and ion homeostasis","description":"Reasoning: The top GO terms are dominated by various transmembrane transport processes (fructose, oxalate, chloride, bicarbonate, sulfate) and by regulation of membrane potential and intracellular pH, plus related processes like gastric acid secretion and sperm capacitation. This pattern points to a cluster of proteins functioning as transporters that maintain ionic balance across membranes. The lone odd term (sensory perception of sound) is not enough to override the transporter theme. ","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007605","count":2},{"id":"GO:0015755","count":1},{"id":"GO:0019532","count":1},{"id":"GO:1902476","count":1},{"id":"GO:0051454","count":1}]},{"hash":"2171252489671265767","title":"Plant Hormone Signaling and Development","description":"These proteins are enriched for plant-specific processes: ABA- and ethylene-activated signaling, seed development, and cutin biosynthesis, alongside multicellular development and transcriptional/ubiquitination regulation. While a NOD-like signaling term appears, the prevailing pattern centers on hormone-regulated plant development, supporting this label.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0060774","count":1}]},{"hash":"1362766184028319336","title":"Rab-dependent endosome-lysosome trafficking and autophagy","description":"This cluster centers on lysosome localization and Rab signaling, with strong emphasis on endosomal transport routes (endosome to Golgi, plasma membrane to endosome) and autophagosome maturation regulation, indicating a cohesive module coordinating vesicular trafficking with autophagy control.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032418","count":1},{"id":"GO:0032486","count":1},{"id":"GO:1901097","count":1},{"id":"GO:1901098","count":1},{"id":"GO:1903527","count":1}]},{"hash":"586473461862372868","title":"Neuronal development and MAPK signaling","description":"This cluster seems centered on neural signaling and development. Key terms include neuron development, retinal ganglion cell axon guidance, VEGF receptor signaling, and ERK/MAPK cascade regulation, which together point to neuronal growth, axon guidance, and signal transduction. Some terms like sperm capacitation and environmental enrichment response are less clearly tied to this theme, but the dominant pattern supports neural development and MAPK signaling as the core function.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000187","count":4},{"id":"GO:0048240","count":4},{"id":"GO:0090648","count":4},{"id":"GO:0048010","count":4},{"id":"GO:0048666","count":4}]},{"hash":"1624847773894632218","title":"Signaling and Cytoskeletal Dynamics","description":"These proteins appear linked by a core theme of signal transduction that governs cytoskeletal remodeling and cell movement, as indicated by GPCR signaling, actin filament bundle assembly, and cell migration terms. Additional terms point to related processes such as membrane localization/trafficking, mechanosensation, cardiac cell communication, and inflammatory signaling, suggesting a broad cluster of signaling events that regulate cytoskeletal dynamics across cell types. Confidence: Medium","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007205","count":5},{"id":"GO:0051017","count":5},{"id":"GO:0086070","count":4},{"id":"GO:1903444","count":4},{"id":"GO:0016477","count":4}]},{"hash":"1401868283176668802","title":"Proteoglycan and glycosaminoglycan biosynthesis","description":"The cluster shows strong signals for proteoglycan biosynthesis (keratan sulfate and heparan sulfate) and related glycosaminoglycan metabolism, plus N-acetylglucosamine modification and sulfation, suggesting roles in extracellular matrix assembly and cell surface proteoglycans.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006044","count":1},{"id":"GO:0006477","count":1},{"id":"GO:0048702","count":1},{"id":"GO:0018146","count":1},{"id":"GO:0042403","count":1}]},{"hash":"858246330061380027","title":"Neuronal signaling and axonogenesis","description":"The cluster\u2019s GO terms cluster around neuronal development and synaptic function, including axonogenesis, glutamatergic synaptic transmission, receptor recycling, and endosome size regulation. The presence of Rho signaling and regulation of kinase activity points to coordinated signaling pathways shaping neuronal connectivity and synaptic trafficking. Although some terms are obsolete, the core theme ties to neuronal development, synaptic communication, and receptor trafficking, making this label representative.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0060316","count":3},{"id":"GO:0007409","count":3},{"id":"GO:0014068","count":3},{"id":"GO:0001881","count":2}]},{"hash":"571920105370566088","title":"Membrane Transport of Ions and Sugars","description":"The Top Terms are dominated by several transmembrane transport processes (nitrite, nitrate, phosphate, sodium, and galactose transport) and a sugar metabolic term (fucose), pointing to membrane transport as the core theme. While transcription-related terms appear, they are less cohesive with the transport signals, so the label centers on the membrane transport function with minor regulatory context.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0015707","count":2},{"id":"GO:0035435","count":2}]},{"hash":"58702629829122514","title":"Inflammatory signaling and chemokine production","description":"This cluster centers on immune signaling and chemokine production: notes on NF-kappaB regulation, macrophage inflammatory protein1/chemokine production, and cell migration point to inflammatory responses. While a few terms touch on other tissues or processes (cardiac signaling, brown fat differentiation), the dominant pattern is inflammation and chemokine-mediated communication.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":5},{"id":"GO:0086070","count":4},{"id":"GO:1903444","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0007253","count":4}]},{"hash":"1067003793049292298","title":"Synaptic vesicle exocytosis and priming","description":"The top GO terms point to presynaptic dense core vesicle exocytosis, synaptic vesicle maturation, neurotransmitter secretion, and synaptic vesicle priming, indicating a cohesive module of neuronal vesicle trafficking and release machinery. Some regulatory terms appear, but the dominant signal is the synaptic vesicle cycle.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0099525","count":3},{"id":"GO:0016188","count":3},{"id":"GO:0007269","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0043314","count":3}]},{"hash":"146222987554615737","title":"NF-kB/NOD2-driven inflammatory signaling and chemokine production","description":"This cluster\u2019s top GO terms cluster around NF-kappaB regulation, NOD2 signaling, and chemokine production (e.g., CCL5, MIP-1 alpha), indicating an innate immune and inflammatory signaling theme. Some terms are obsolete, but the core trend points to NF-kB/NOD2-mediated inflammatory responses and chemokine expression.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":5},{"id":"GO:0070431","count":5},{"id":"GO:0086070","count":4},{"id":"GO:1903444","count":4},{"id":"GO:0007253","count":4}]},{"hash":"2000147748327331279","title":"Unknown","description":"The top terms cover a broad and seemingly unrelated mix: DNA replication, development (mesoderm formation and dorsal/ventral neural tube patterning), ER protein folding, nuclear export, and various immune/stress responses (interferon-beta production, xenophagy, dsRNA response, LPS signaling). There is no single cohesive functional theme across these terms, and the cluster has no edges, making it unclear how the proteins function as a unit. ","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0034975","count":2},{"id":"GO:0071374","count":2},{"id":"GO:0001707","count":2}]},{"hash":"194786474010541464","title":"Unknown","description":"The cluster shows a mix of transcription regulation terms (RNA polymerase II) alongside neural development, signaling, and metabolic processes (hippocampus development, dendritic spine morphogenesis, bile acid secretion, Rho signaling, stress granule localization, and heart action potential) with no edges connecting the proteins (Edges: 0, Triangles: 0, Max Degree: 0). This lack of a single cohesive function or pathway makes it unclear what unifying theme ties the proteins together, so a cautious Unknown label is appropriate.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":2},{"id":"GO:0045128","count":2},{"id":"GO:0034244","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0021766","count":2}]},{"hash":"1563303117815290093","title":"Cardiovascular development and calcium signaling","description":"The top GO terms cluster around heart development, branching of blood vessels, and cardiac hypertrophy, alongside regulation of calcium signaling (voltage-gated calcium channels and guanylate cyclase). This suggests a coherent theme of cardiovascular development and calcium-dependent signaling, with some auxiliary terms related to microtubule dynamics and cellular responses that are common in developmental processes.","confidence":"High","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901387","count":3},{"id":"GO:1903087","count":3},{"id":"GO:0007020","count":3},{"id":"GO:0001569","count":2},{"id":"GO:0060291","count":2}]},{"hash":"1916469219692119723","title":"Unknown","description":"Top terms are diverse and largely unrelated, including hormone responses (gibberellin, abscisic acid), chromatin/telomere regulation, DNA repair, transcription, and viral processes. With no edges connecting proteins, there is no clear shared function across the cluster. Thus, label as Unknown with None.","confidence":"","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009739","count":5},{"id":"GO:1900033","count":5},{"id":"GO:1990414","count":5},{"id":"GO:1905778","count":5},{"id":"GO:0016032","count":5}]},{"hash":"1230637967816682470","title":"Transcription Regulation and Redox Homeostasis","description":"This cluster is dominated by transcription-related GO terms (DNA-templated transcription, negative regulation of transcription by RNA polymerase II, and positive regulation of DNA binding) with supporting redox-related terms (oxidation-reduction, cell redox homeostasis) and ER stress. Together they suggest nuclear factors that regulate gene expression in response to cellular redox state and stress, making this label appropriate. Annotation noise is possible due to obsolete terms and a few unrelated items, but the core theme centers on transcriptional control linked to redox/ER stress.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0006351","count":5},{"id":"GO:0045454","count":5},{"id":"GO:0033158","count":4},{"id":"GO:0034976","count":4}]},{"hash":"456238927361959151","title":"Carbohydrate Metabolism and PPP Regulation","description":"Explanation: The top GO terms are dominated by carbohydrate metabolism\u2014fructose metabolic process, fructose 2,6-bisphosphate metabolic process, carbohydrate phosphorylation, and regulation of the pentose-phosphate shunt\u2014along with related glucose/lactate pathways. A few terms (photosynthesis, PQQ biosynthetic process, cobalt response, apoptosis regulation) are more peripheral but can be contextualized within metabolic or stress-related processes in certain organisms. Overall, the cluster centers on sugar processing and related redox metabolism.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":2},{"id":"GO:0043065","count":2},{"id":"GO:0015979","count":2},{"id":"GO:0018189","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1249137161987204363","title":"Chloroplast protein import and PSII assembly","description":"The cluster\u2019s GO terms cluster around chloroplast targeting and photosynthetic machinery, including protein import into the chloroplast\u2019s thylakoid membrane and stroma, thylakoid organization, and photosystem II assembly, with related chlorophyll turnover and stress signaling processes (ROS regulation, stomatal responses). This points to a cohesive theme of chloroplast-directed proteins involved in photosynthesis and chloroplast-associated stress signaling, despite some auxiliary terms.","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010182","count":1},{"id":"GO:0045038","count":1},{"id":"GO:2000070","count":1},{"id":"GO:0045037","count":1},{"id":"GO:1903426","count":1}]},{"hash":"1980861066064149412","title":"Nucleotide metabolism and RNA processing","description":"The top GO terms are dominated by nucleotide catabolic processes (dADP, diadenosine pentaphosphate, IDP, diphosphoinositol polyphosphate) and RNA-related activities (adenosine to inosine editing; negative regulation of rRNA processing), suggesting the proteins cluster around nucleotide turnover and RNA modification/processing rather than a single cohesive pathway. Some terms like cytochrome b6f complex assembly or IPP biosynthesis appear less central or incidental. ","confidence":"Medium","size":21,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010190","count":2},{"id":"GO:0009240","count":2},{"id":"GO:1901907","count":2},{"id":"GO:2000781","count":2},{"id":"GO:0046057","count":2}]},{"hash":"1443941414893521388","title":"Plant Chromatin Remodeling and Genome Stability","description":"Top GO terms cluster around chromatin remodeling, heterochromatin formation, telomere establishment, and genome maintenance processes, with supporting hints from hormone signaling (ABA, GA) that situate these nuclear functions in a plant context. This suggests a cohesive theme of chromatin regulation linked to genome stability in plants, despite some auxiliary terms like viral processes. ","confidence":"Medium","size":20,"edges":7,"triangles":0,"max_degree":3,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009737","count":7},{"id":"GO:0016032","count":7},{"id":"GO:0043044","count":7},{"id":"GO:0009739","count":6},{"id":"GO:1900033","count":6}]},{"hash":"1965961005097017369","title":"Bacterial DNA replication and SOS response","description":"Most terms cluster around prokaryotic DNA replication and DNA damage response: DNA replication, unwinding, rolling-circle replication, bacterial-type replication, and homologous recombination repair, with the SOS response signaling DNA damage. A few terms also touch on defense against foreign DNA. This supports labeling the cluster as bacterial DNA replication and SOS response.","confidence":"High","size":20,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009432","count":7},{"id":"GO:0006268","count":7},{"id":"GO:0006260","count":5},{"id":"GO:0090305","count":5},{"id":"GO:0032508","count":5}]},{"hash":"1245171387681415165","title":"Transcriptional Repression and NF-kappaB Signaling","description":"Enriched GO terms point to repression of transcription by RNA Pol II, histone catabolic processes, and protein ubiquitination, alongside activation steps in the NF-kappaB pathway (I-kappaB phosphorylation and NIK activity). This suggests a cluster of proteins involved in gene expression regulation and signaling that modulates cell survival and chromatin dynamics. Some terms (manganese ion transport, dosage compensation, Wnt receptor catabolic process) appear as outliers and may reflect annotation noise or multifunctionality. ","confidence":"Medium","size":20,"edges":13,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0006828","count":2},{"id":"GO:0036205","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0090073","count":1}]},{"hash":"1662361357390514707","title":"Hematopoiesis and Mitochondrial Metabolism","description":"The top GO terms point to hematopoietic differentiation (regulation of erythrocyte and megakaryocyte development) alongside metabolic processes essential for energy and cofactor biosynthesis (thiamine and heme biosynthesis, mitochondrial electron transport), suggesting the cluster reflects metabolism supporting blood cell development rather than a single signaling pathway. Some neurotransmitter-related terms appear but are secondary to the hematopoietic/metabolic theme.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0009228","count":12},{"id":"GO:0006782","count":9},{"id":"GO:0043046","count":9},{"id":"GO:0010725","count":8},{"id":"GO:0014063","count":8}]},{"hash":"989479899081727412","title":"Genome maintenance and embryonic development","description":"The top GO terms show strong DNA replication and DNA repair, indicating genome maintenance functions, alongside several embryonic development processes (cardiac differentiation, cranial skeleton morphogenesis, lung mesenchyme development, corpus callosum development) as well as cell migration and apoptotic regulation, suggesting a cluster of proteins that link genome maintenance with developmental signaling.","confidence":"Medium","size":20,"edges":106,"triangles":285,"max_degree":17,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0006260","count":20},{"id":"GO:0006281","count":20},{"id":"GO:2000727","count":20},{"id":"GO:0048701","count":20},{"id":"GO:0016477","count":19}]},{"hash":"802460959812758911","title":"Unknown","description":"The top GO terms are a mix of immune responses (innate and defense to virus), neural development/behavior (corticospinal tract morphogenesis, vocalization behavior, neurotransmitter loading into vesicles), and various transport/metabolic processes (vitamin transport, ascorbate metabolism, sugar/trehalose transport). This broad, disparate set provides no single coherent function to unite the cluster, so an Unknown label is most appropriate.","confidence":"","size":20,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0051607","count":2},{"id":"GO:0021957","count":2},{"id":"GO:0071625","count":2},{"id":"GO:0035461","count":2}]},{"hash":"2075214785556781960","title":"Membrane Transporters and Vesicular Loading","description":"This cluster is driven by GO terms for transmembrane transport of ions, sugars, nitrite/nitrate, and vitamins, plus a vesicular transport process (neurotransmitter loading into synaptic vesicles). The common theme is membrane-associated transport activities and vesicle loading, suggesting a cohesive group of transporter proteins and related vesicular machinery.","confidence":"High","size":20,"edges":91,"triangles":161,"max_degree":18,"top_function":null,"top_go_terms":[{"id":"GO:0006935","count":2},{"id":"GO:0015707","count":2},{"id":"GO:0035435","count":2},{"id":"GO:0015706","count":2},{"id":"GO:0006004","count":2}]},{"hash":"772170712758595595","title":"Ion and sugar transmembrane transport","description":"Based on the top GO terms, the cluster is enriched for transmembrane transport of various solutes, including phosphate, nitrite/nitrate, sodium ions, and sugars like galactose and fucose. This points to a membrane transport role for diverse solutes. Some terms are regulatory or outdated annotations (stress response mRNA stability, viral process, obsolete antibiotic transport) and may reflect noise or pleiotropy, but the dominant signal supports a transport-focused theme.","confidence":"Medium","size":20,"edges":17,"triangles":2,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":3},{"id":"GO:0010610","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0015707","count":2}]},{"hash":"840209798415184520","title":"Developmental and Metabolic Regulation","description":"The cluster includes GO terms tied to multicellular development, neuron maturation, and stem cell proliferation, indicating roles in growth and differentiation. It also includes several metabolic and biosynthetic processes (thiamine, tryptophan, camphor catabolism) and ion transport, suggesting regulation of cellular metabolism and signaling. The combination points to proteins that regulate development and metabolism rather than a single pathway, so a broad label is appropriate.","confidence":"Medium","size":20,"edges":42,"triangles":0,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0071805","count":2},{"id":"GO:0046886","count":2},{"id":"GO:0006569","count":2},{"id":"GO:0009228","count":2}]},{"hash":"1313681374683240244","title":"ER-Golgi trafficking and ubiquitination","description":"The top terms point to vesicle transport between the ER and Golgi (anterograde and retrograde), ER lumen protein retention, and ubiquitin-related modification/degradation (polyubiquitination, autoubiquitination). These together suggest a functional cluster centered on ER-Golgi trafficking and protein quality control via ubiquitination, with one term related to membrane protein localization as a peripheral note.","confidence":"Medium","size":20,"edges":14,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0090004","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0071340","count":1},{"id":"GO:0006890","count":1},{"id":"GO:0006621","count":1}]},{"hash":"2243285744520902417","title":"MVB/ESCRT Vesicle Trafficking and Exosome Regulation","description":"GO terms point to ESCRT- and multivesicular body\u2013mediated trafficking, including endosome-to-lysosome transport via MVB sorting, viral budding via ESCRT, and regulation of exosomal secretion, suggesting a coherent vesicle trafficking/exosome biology theme. Some terms are peripheral (sterol metabolism, cytokinesis), and no protein\u2013protein interactions are observed, so the label is supported but not universally definitive. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060325","count":2},{"id":"GO:0051260","count":1},{"id":"GO:0000281","count":1},{"id":"GO:0032510","count":1},{"id":"GO:0090611","count":1}]},{"hash":"1856480188314612049","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030836","count":1},{"id":"GO:0046196","count":1},{"id":"GO:0006114","count":1},{"id":"GO:0032361","count":1},{"id":"GO:0071318","count":1}]},{"hash":"1908403319617082967","title":"RNA Pseudouridylation Enzymes","description":"The top GO terms cluster around pseudouridine synthesis in multiple RNA types (snRNA, tRNA, rRNA, mRNA) and related RNA modification/editing processes (methylation, thio-modification, editing). This points to a group of enzymes specialized in installing pseudouridines and associated RNA modifications. A distant thiamine biosynthesis term appears but does not redefine the cluster.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031120","count":2},{"id":"GO:0031119","count":2},{"id":"GO:1990481","count":2},{"id":"GO:0000455","count":1},{"id":"GO:0030488","count":1}]},{"hash":"1286126589875420443","title":"Unknown","description":"The top terms reflect immunity (muramyl dipeptide response, B cell receptor signaling), development (lung-associated mesenchyme, corpus callosum development, embryonic cleavage), metabolism (triglyceride catabolic process), and basic cellular processes (rRNA maturation, amyloid precursor protein biosynthetic regulation, superoxide generation), with no single unifying function across the 20 proteins. This lack of a coherent theme suggests there is no clear label beyond Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032495","count":2},{"id":"GO:0042985","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0032929","count":1},{"id":"GO:0040016","count":1}]},{"hash":"1215833472055219546","title":"Ubiquitination-Driven Regulation of Cell Fate","description":"Top GO terms are dominated by protein polyubiquitination and broad regulatory processes (cell cycle, transcription, apoptosis/necroptosis, Toll-like receptor signaling). The inclusion of development, migration, telomere capping, and muscle stretch responses suggests these proteins function as regulators that modulate diverse cellular outcomes through ubiquitin-mediated signaling, rather than a single pathway. This points to a general theme of ubiquitin-dependent control of cell fate and signaling networks.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000209","count":9},{"id":"GO:0071157","count":7},{"id":"GO:0034121","count":7},{"id":"GO:0000122","count":7},{"id":"GO:0043066","count":7}]},{"hash":"554906029531925705","title":"DNA Replication & Cell Cycle Machinery","description":"This cluster is dominated by GO terms related to DNA replication initiation, the pre-replicative complex, and overall cell cycle progression ( initiation, replication, G1/S transition, and replication-associated repair). The overlap of initiation and replication processes with cell cycle regulation suggests the proteins function together in preparing and carrying out DNA replication during the cell cycle, with a minor presence of obsolete terms likely reflecting annotation history.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0006270","count":1},{"id":"GO:0006260","count":1},{"id":"GO:1902977","count":1},{"id":"GO:0006267","count":1}]},{"hash":"171947424160228184","title":"Chromatin regulation and histone modification","description":"The cluster is strongly enriched for chromatin-related processes: heterochromatin formation and maintenance, negative regulation of transcription by RNA polymerase II, various histone modification activities (histone H4-R3 methylation, peptidyl-arginine methylation), and nucleosome density/rRNA methylation. These converge on controlling chromatin state and transcription, which can also influence cell growth and senescence. While a few terms (e.g., cobalamin biosynthesis) are less directly tied, the dominant theme is chromatin regulation and epigenetic control of gene expression.","confidence":"High","size":20,"edges":156,"triangles":698,"max_degree":19,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000122","count":7},{"id":"GO:0000183","count":6},{"id":"GO:0060303","count":5},{"id":"GO:0043985","count":5},{"id":"GO:0016049","count":5}]},{"hash":"1868244355406698824","title":"Neural development and stress-signaling cluster","description":"Explanation: The top GO terms cluster around neural development (neural tube closure, corpus callosum development) and cell movement, with signaling and regulatory processes such as JNK cascade regulation, DNA replication, and apoptosis. While some terms relate to immune or stress responses (B cell receptor signaling, viral response, amino acid starvation), the strongest theme centers on development-related signaling and cell fate regulation, particularly in neural contexts.","confidence":"Medium","size":20,"edges":138,"triangles":519,"max_degree":19,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":19},{"id":"GO:0046330","count":19},{"id":"GO:0016477","count":18},{"id":"GO:0010898","count":18},{"id":"GO:0022038","count":18}]},{"hash":"385902843384268374","title":"Bacterial lipid and secondary metabolite biosynthesis","description":"The top GO terms cluster around lipid/fatty acid metabolism (fatty acid biosynthetic process, medium-chain fatty acid transport, PHB biosynthesis) and small-molecule or nonribosomal peptide biosynthesis (amino acid activation for nonribosomal peptide biosynthetic process), with several catabolic pathways (phenylacetate, malonate) and even an antibiotic response signal. Taken together, these terms suggest a metabolism-focused cluster centered on lipid/secondary metabolite production and related pathways rather than signaling or transport alone. Some outliers and obsolete terms exist, but the overall theme is coherent around lipid and secondary metabolite biosynthesis and processing.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":8},{"id":"GO:1902987","count":4},{"id":"GO:0042619","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0010124","count":3}]},{"hash":"576457523815211164","title":"ER-to-Golgi vesicle transport","description":"This cluster centers on proteins involved in the secretory pathway, especially ER-to-Golgi vesicle transport and related intracellular trafficking (ER to Golgi, endosome-to-Golgi retrograde transport, and broader intracellular protein transport). A few terms are obsolete or represent unrelated processes (osteoblast differentiation, apoptotic signaling, ubiquitin-dependent catabolism), but the dominant signal is vesicle trafficking between ER and Golgi and associated retrograde routes.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":2},{"id":"GO:0015031","count":1},{"id":"GO:0042147","count":1},{"id":"GO:0035584","count":1},{"id":"GO:1904154","count":1}]},{"hash":"1622479611106537211","title":"Steroid and Retinoid Metabolism in Development","description":"The top GO terms cluster around retinol metabolic process, androgen metabolism/catabolic processes, and glucocorticoid biosynthesis, all pointing to metabolism of steroid/retinoid hormones with a developmental context, notably lung development. While there are also broader terms like regulation of transcription and cell division, the strongest common thread is hormone and vitamin A\u2013related metabolism linked to developmental processes, suggesting this label. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0042572","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0051301","count":4},{"id":"GO:0008209","count":3}]},{"hash":"2203365208233010945","title":"Diverse Membrane Transport","description":"This cluster is dominated by GO terms referencing transport and export across membranes, including xenobiotic export, peroxisomal fatty acid import, vacuolar ion import, teichoic acid and bacteriocin transport, and oligopeptide export from mitochondrion. While there are a few outlier terms (ABA signaling in stomatal movement, nucleotide-excision repair) that may reflect noise or multi-function proteins, the common thread appears to be membrane-associated transport of diverse substrates. Confidence in this label is Medium.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046618","count":3},{"id":"GO:0060081","count":3},{"id":"GO:1901527","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0015910","count":3}]},{"hash":"483616529867404676","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0033050","count":1},{"id":"GO:0046300","count":1},{"id":"GO:0006151","count":1},{"id":"GO:0045329","count":1}]},{"hash":"2008355920394968828","title":"Ribosome Biogenesis and Translation Machinery","description":"Strong enrichment for ribosome biogenesis, cytoplasmic translation, translation, and ribosomal large subunit export from the nucleus indicates a core cluster of ribosome assembly and function. Additional tRNA modification and cell cycle terms suggest coordination with growth, but the dominant theme is ribosome production and protein synthesis.","confidence":"High","size":20,"edges":139,"triangles":557,"max_degree":19,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":9},{"id":"GO:0002181","count":8},{"id":"GO:0006412","count":8},{"id":"GO:0000055","count":7},{"id":"GO:1903833","count":7}]},{"hash":"2258968722629158009","title":"Galactose and Carbohydrate Metabolism","description":"The top GO terms cluster around sugar processing, especially galactose-related pathways: cellular response to glucose stimulus, glycolytic processing from galactose, galactitol and D-galacturonate metabolism, and broader carbohydrate phosphorylation, all pointing to a coherent theme of carbohydrate metabolism with a focus on galactose. A couple of peripheral terms on ubiquitin-dependent proteolysis and polyamine biosynthesis may reflect broader regulatory processes. Overall, the label captures the dominant functional theme of the cluster.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071333","count":2},{"id":"GO:0071596","count":1},{"id":"GO:0071233","count":1},{"id":"GO:1901718","count":1},{"id":"GO:0000435","count":1}]},{"hash":"207691533315895671","title":"Mitochondrial Transport and Energetics","description":"The top GO terms converge on mitochondrial inner-m membrane processes: transport of ADP, ATP, alpha-ketoglutarate, and magnesium; regulation of membrane permeability and membrane potential; and responses to oxidative stress, plus insulin/IGF signaling related metabolic regulation. This cluster appears to represent a module of mitochondrial metabolite transport coupled to energy production and redox homeostasis, justifying the name.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":4},{"id":"GO:0051881","count":4},{"id":"GO:0015742","count":4},{"id":"GO:0032869","count":4},{"id":"GO:1990314","count":4}]},{"hash":"1493234958263980644","title":"Cofactor and lipid biosynthesis","description":"This cluster centers on multiple biosynthetic pathways for cofactors and lipids (cobalamin, heme/porphyrins, isoprenoids, cholesterol, and ethanolamine metabolism) and includes an energy metabolism term (mitochondrial ATP synthesis). Translation appears as a less cohesive signal but may reflect general housekeeping function prevalent in this group. ","confidence":"Medium","size":20,"edges":183,"triangles":1035,"max_degree":19,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0009236","count":3},{"id":"GO:0006779","count":2},{"id":"GO:0006580","count":2},{"id":"GO:0042775","count":1}]},{"hash":"321850239333892864","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0045292","count":5},{"id":"GO:0006378","count":5},{"id":"GO:0098789","count":4},{"id":"GO:0034247","count":4},{"id":"GO:0009432","count":3}]},{"hash":"1697910035254354989","title":"Cardiac development and integrin signaling","description":"The top GO terms consistently point to heart development and integrin-related adhesion/signaling (e.g., heart development, integrin activation, regulation of integrin activation, cell migration, and SA node cell communication). While there are some miscellaneous or obsolete terms in the list, the core signal centers on cardiac tissue formation and integrin-mediated adhesion/migration, suggesting a cohesive theme around cardiac development and adhesion signaling. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061408","count":2},{"id":"GO:0090162","count":2},{"id":"GO:0086070","count":1},{"id":"GO:0033623","count":1},{"id":"GO:0007507","count":1}]},{"hash":"961441645630689461","title":"Plant photosynthesis components","description":"Top GO terms are photosynthesis and photosynthesis, light reaction (2 annotations each), suggesting these proteins are chloroplast/plants-associated and function in the light-dependent reactions of photosynthesis. The presence of unrelated or obsolete terms likely reflects annotation noise or cross-species data, but the core theme remains photosynthesis.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015979","count":2},{"id":"GO:0019684","count":2},{"id":"GO:0032770","count":1},{"id":"GO:1901206","count":1},{"id":"GO:0031284","count":1}]},{"hash":"2071569454998883239","title":"Unknown","description":"The top GO terms span dephosphorylation, toxic-substance response, mechanosensory detection in touch, B cell receptor signaling, fatty-acid response, phototropism, development, actin ubiquitination, TNF signaling, and broad binding regulation, indicating no single shared function. With zero edges/triangles, there is no apparent interaction pattern to tie these terms into a cohesive pathway, so a specific functional label cannot be assigned.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016311","count":4},{"id":"GO:0009636","count":4},{"id":"GO:1905789","count":3},{"id":"GO:0050853","count":3},{"id":"GO:0070542","count":3}]},{"hash":"67606154103714494","title":"TLR Signaling and Innate Immunity","description":"The terms cluster around Toll-like receptor signaling pathways (TLR6/8/9), the Toll signaling pathway, and responses to fungal and bacterial lipopeptide, indicating enrichment for innate immune sensing via TLRs. A few terms related to neural processes (synapse assembly, dopamine response, corpus callosum development) may reflect broader roles of TLR signaling in neural development or signaling, but the dominant signal is Toll-like receptor\u2013mediated immunity.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009620","count":2},{"id":"GO:0071726","count":2},{"id":"GO:0034162","count":2},{"id":"GO:0051965","count":2},{"id":"GO:1902499","count":2}]},{"hash":"56025202549493171","title":"Heat Stress Response and ER Protein Folding","description":"Top terms reveal a cohesive theme around heat response and ER protein folding, pointing to proteostasis under stress. Additional terms ( xenobiotic response, calcium signaling, and regulation of heat response) reflect broader stress-regulation, but the most representative function is heat-related protein quality control.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0035690","count":2},{"id":"GO:0071277","count":2},{"id":"GO:0006260","count":2}]},{"hash":"2206898589529442178","title":"Nuclear Transport and Transcription Regulation","description":"GO terms show multiple nuclear transport events (RNA import into nucleus, snRNP import, transcription factor import, ribosomal subunit export) and transcription regulation, suggesting a functional theme around nuclear trafficking and gene expression control. Other terms appear less connected (phototaxis, neuron signaling, axis polarity, mitotic movement), likely annotation noise, but the dominant signal is nuclear transport and transcription control.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042331","count":2},{"id":"GO:0006404","count":2},{"id":"GO:0010226","count":2},{"id":"GO:0006608","count":1},{"id":"GO:0000055","count":1}]},{"hash":"737470799160981336","title":"Telomere maintenance and chromosome localization","description":"The top GO terms cluster around telomere biology\u2014maintenance, capping, and localization to telomeric regions\u2014indicating a common theme of chromosome end protection. A couple terms reference other processes (cell cycle and muscle/bud processes) that are less coherent with the core telomere theme, which gives only moderate confidence in the label.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007120","count":2},{"id":"GO:0048741","count":2},{"id":"GO:0098907","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0000086","count":2}]},{"hash":"1134505232599713920","title":"Growth and differentiation with angiogenesis and cell migration","description":"These proteins show enrichment for cell growth and angiogenesis-related proliferation, plus cell migration and differentiation of neural and immune lineages (cerebellar granule cell differentiation and follicular dendritic cell differentiation). The dominant theme centers on developmental growth and vascular/lineage-specific differentiation, with some noise terms present. Confidence: Medium","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":4},{"id":"GO:1903589","count":3},{"id":"GO:0009408","count":3},{"id":"GO:0033028","count":3},{"id":"GO:2000031","count":3}]},{"hash":"1827886677905455626","title":"Immune and stress response regulators","description":"This cluster is enriched for GO terms describing innate immune response to lipopolysaccharide, diverse stress responses (hypoxia, metal- and chemical-induced stresses such as glucocorticoids and arsenic), and a transcriptional regulatory role (negative regulation of RNA polymerase II) alongside a signaling pathway (Wnt). The combination points to a group of proteins that coordinate signaling and transcriptional responses under stress or immune challenges rather than a single, unitary function.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032496","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0016055","count":2},{"id":"GO:0043200","count":1},{"id":"GO:0010039","count":1}]},{"hash":"1076660746826575711","title":"Unknown","description":"The Top Terms span glycolysis, detoxification, chlorophyll catabolic and various biosynthetic processes, RNA methylation/capping, and stress/response terms (tumor cell and cocaine). This broad mix lacks a single cohesive function or pathway, so a specific, representative label cannot be assigned with confidence.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0015996","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0017000","count":2}]},{"hash":"34836171970136403","title":"Vesicle trafficking to Golgi and endosomes","description":"The top GO terms concentrate on intracellular transport, COPII vesicle cargo loading, recycling endosome-to-Golgi transport, and Rab signaling regulation, plus general intracellular protein transport. This suggests a cohesive cluster of proteins involved in vesicle formation, trafficking, and fusion within the Golgi\u2013endosome system, with some broader transport-regulation roles.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902543","count":1},{"id":"GO:0035526","count":1},{"id":"GO:1902018","count":1},{"id":"GO:0031030","count":1},{"id":"GO:0031338","count":1}]},{"hash":"1660484565190081242","title":"Histone modification and transcription regulation","description":"This cluster centers on GO terms for histone modifications (e.g., methylation of H3K4, H3K36; H4K16 acetylation, H3K79 methylation) and regulation of DNA-templated transcription, indicating a cohesive role in epigenetic control of gene expression. Some terms are listed as obsolete, but the core theme remains chromatin state modification influencing transcription. The lack of edges doesn\u2019t undermine this interpretation, as the shared functional context is clear among the proteins.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":3},{"id":"GO:0006349","count":2},{"id":"GO:0070544","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0048705","count":2}]},{"hash":"1565308054936234969","title":"Photosynthesis Light Response and Photoprotection","description":"This cluster is dominated by GO terms related to photosynthesis, light harvesting in photosystem II, nonphotochemical quenching, and various light-response processes (UV-A, red light, high/low light). These terms indicate a cohesive theme of light-driven photosynthetic activity and photoprotection, suggesting the proteins function together in photosynthesis and light-stimulated stress responses; a few outliers like mRNA processing are present but do not define the overall theme.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071492","count":3},{"id":"GO:0006397","count":2},{"id":"GO:0071486","count":2},{"id":"GO:0009645","count":2},{"id":"GO:0018298","count":2}]},{"hash":"1936152498332288688","title":"Synapse Organization and Plasticity","description":"The proteins cluster around synaptic processes: synapse organization, protein and receptor localization to the synapse, and synaptic structural plasticity, along with actin cytoskeleton remodeling\u2014all hallmark features of neural signaling and synapse maintenance. While a couple of terms (e.g., bile acid secretion and some obsolete annotations) are peripheral or noisy, the dominant signal points to synaptic assembly, localization, and plasticity, with implications for exploration behavior and neural development.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035640","count":5},{"id":"GO:0032416","count":4},{"id":"GO:0050808","count":4},{"id":"GO:1901206","count":4},{"id":"GO:0035418","count":4}]},{"hash":"2133450004901612051","title":"Unknown","description":"The top GO terms are diverse, including protein homooligomerization, ubiquitination, cellulose/xylan catabolism, neurotransmitter transport, insulin stimulus response, and mitochondrial membrane regulation. There is no single cohesive function linking these terms, suggesting a heterogeneous set of roles rather than a unified cluster. Therefore, I cannot assign a specific, representative label; Unknown with None confidence. ","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0016567","count":4},{"id":"GO:0030245","count":3},{"id":"GO:0006836","count":3},{"id":"GO:2000372","count":3}]},{"hash":"786901995099673025","title":"Unknown","description":"The GO terms span markedly different processes: skeletal muscle regeneration, DNA repair by homologous recombination, mitotic chromatid cohesion, adipocyte differentiation, endothelial cell proliferation and angiogenesis, heat response, myeloid apoptosis, salicylic acid signaling, cell migration, and NF-kappaB cytoplasmic sequestration. With no clear overarching pathway or function and no network connections (0 edges), there is no single cohesive theme to bind these proteins into a meaningful, specific label. Therefore the cluster is best described as Unknown.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043403","count":3},{"id":"GO:0000724","count":2},{"id":"GO:0007064","count":2},{"id":"GO:0045444","count":2},{"id":"GO:1903589","count":2}]},{"hash":"1058532558675783126","title":"Unknown","description":"Unknown","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042952","count":2},{"id":"GO:0006006","count":2},{"id":"GO:0006098","count":2},{"id":"GO:0061158","count":1},{"id":"GO:0010875","count":1}]},{"hash":"802214988620440227","title":"Unknown","description":"The GO terms span diverse biological processes\u2014cell cycle regulation, transcription, development (axis determination, heart looping), and various endocrine activities (renin secretion, insulin processing, LDL receptor-related processes)\u2014with no clear, single functional theme tying the proteins together. Additionally, there are no edges among the proteins, suggesting a heterogeneous set rather than a cohesive pathway. ","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904908","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0007354","count":2}]},{"hash":"1310634331517607212","title":"RNA Methylation and Processing","description":"The top GO terms cluster around methylation events across RNA species (tRNA and rRNA methylation, rRNA modification) plus mRNA capping and histone methylation, indicating a shared function in RNA and chromatin modification. Some biosynthetic terms appear incidental, but the dominant theme is methyltransferase-related activities involved in RNA processing and epigenetic marks.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0009102","count":6},{"id":"GO:0030488","count":5},{"id":"GO:0070476","count":5},{"id":"GO:0006370","count":4}]},{"hash":"382883723266430669","title":"Methylation-Associated Biosynthetic Enzymes","description":"The top GO terms are dominated by methylation activities (peptidyl-lysine dimethylation, rRNA methylation, N-terminal peptidyl-glycine methylation), suggesting methyltransferase functions. Additional terms point to diverse biosynthetic processes (biotin, menaquinone, antibiotic biosynthesis, and proteoglycan biosynthesis), implying roles in various biosynthetic pathways that may involve methylation or modification. While a unifying theme around methylation in biosynthesis is plausible, the terms are heterogeneous and there are no interaction edges, so the cohesion is tentative.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018027","count":3},{"id":"GO:0031167","count":3},{"id":"GO:0018013","count":3},{"id":"GO:0009102","count":3},{"id":"GO:0017000","count":3}]},{"hash":"716006398012225155","title":"Multisystem Developmental Processes","description":"The GO terms cluster around developmental and morphogenetic themes across multiple organ systems (kidney: glomerular basement membrane development, glomerular filtration; nervous system: CNS development, innervation; cartilage: chondrocyte development; smooth muscle: esophagus smooth muscle contraction), with additional signaling regulation context (negative regulation of FGFR signaling). An outlier term (lipoteichoic acid biosynthetic process) may reflect annotation noise. The absence of edges suggests these proteins group by shared developmental roles rather than direct interactions, supporting a multisystem development label.","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032836","count":3},{"id":"GO:0003094","count":3},{"id":"GO:0060686","count":3},{"id":"GO:0007417","count":3},{"id":"GO:0060384","count":3}]},{"hash":"1092858294827718394","title":"Selenocysteine incorporation and translation-associated tRNA processing","description":"The top terms are dominated by translation and selenocysteine biology (translation, selenocysteine incorporation, Sec-tRNA biosynthesis, tRNA transamidation), suggesting this cluster centers on the translation machinery with a emphasis on selenocysteine-containing tRNAs and related tRNA maturation steps; a couple of unrelated catabolic terms may be noise.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071952","count":1},{"id":"GO:0016259","count":1},{"id":"GO:0097056","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0001514","count":1}]},{"hash":"122107627016294642","title":"Unknown","description":"The terms span chromatin modification (histone deacetylation), transcriptional regulation, and stress- or nutrient-responsive behaviors (biofilm adhesion, anoikis regulation, invasive growth), with no single cohesive function tying them together, and the cluster has no edges to reinforce a shared role.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000210","count":1},{"id":"GO:1900526","count":1},{"id":"GO:1900525","count":1},{"id":"GO:0061408","count":1},{"id":"GO:0016575","count":1}]},{"hash":"1683286064051432864","title":"Unknown","description":"The top terms are highly diverse, including capsule polysaccharide biosynthesis, xenobiotic and ethanol response, and several cytoskeleton/centrosome-related terms, with no connecting pathway across all proteins and no edges. This prevents a coherent common function to label the cluster; only a subset hints at cytoskeleton remodeling or inheritance, which is not representative of the whole set.","confidence":"","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045227","count":2},{"id":"GO:0010735","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0045471","count":2},{"id":"GO:0000147","count":1}]},{"hash":"478241311296405693","title":"Nucleic acid processing and repair","description":"These proteins show a coherent signal for nucleic acid metabolism, with emphasis on tRNA modification and regulation of translation (tRNA wobble modification, regulation of translational initiation by tRNA modification), plus mRNA processing and multiple DNA/RNA repair terms. The combination suggests a module focused on nucleic acid maintenance and processing, with occasional links to cell death pathways via mitochondrial permeability, but the core theme remains genome and RNA integrity. ","confidence":"Medium","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990983","count":1},{"id":"GO:1902445","count":1},{"id":"GO:0035553","count":1},{"id":"GO:0006281","count":1},{"id":"GO:0012501","count":1}]},{"hash":"1303718952732478417","title":"TLR-Mediated Inflammation","description":"Based on GO terms, this cluster centers on Toll-like receptor signaling and inflammatory responses, including responses to fungi and downstream cytokine production. The presence of multiple TLR pathways (TLR8, TLR9, TLR10) and signaling (Toll signaling) with regulatory terms for interferon and IL-18 production suggests a coherent innate immune signaling module driven by TLRs.","confidence":"High","size":20,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0006954","count":3},{"id":"GO:0009620","count":2},{"id":"GO:0034162","count":2},{"id":"GO:1902499","count":2},{"id":"GO:1903351","count":2}]},{"hash":"135333823635351562","title":"Ubiquitin-Dependent Protein Degradation","description":"The cluster is dominated by GO terms related to ubiquitination and protein turnover, including ubiquitin-dependent protein catabolic process, ERAD, and autoubiquitination, with related effects on signaling and receptor turnover, indicating a cohesive theme around ubiquitin-proteasome\u2013mediated degradation.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":5},{"id":"GO:0030433","count":4},{"id":"GO:0036205","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0090073","count":3}]},{"hash":"1124989644942449251","title":"Oxidative stress detoxification and DNA repair","description":"The cluster is enriched for redox- and detoxification-related GO terms (cellular oxidant detoxification, glutathione metabolic process, cell redox homeostasis, toxin catabolic process) and also includes nucleotide-excision repair, plus stress-related responses (response to starvation, metal ion response). This points to a cohesive theme of cellular defense against oxidative/chemical stress, tying detox pathways to DNA repair processes in the cluster. ","confidence":"Medium","size":19,"edges":118,"triangles":506,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":11},{"id":"GO:0006289","count":10},{"id":"GO:0006749","count":9},{"id":"GO:0009072","count":9},{"id":"GO:0009407","count":9}]},{"hash":"681112067418199341","title":"Ubiquitin-Dependent Protein Quality Control (ERAD)","description":"The top GO terms center on ubiquitination processes (K63-linked ubiquitination, autoubiquitination) and the ubiquitin-dependent ERAD pathway, suggesting a cluster focused on tagging proteins for degradation and ER-associated quality control, with some accompanying chaperone-related activity; other terms appear as ancillary stress-related signals.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0071361","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0090035","count":4}]},{"hash":"2082371759536211313","title":"Growth and differentiation signaling cluster","description":"The terms point to signaling pathways that control cell growth, proliferation, and differentiation (notably Wnt and Hippo signaling, apoptosis regulation, and keratinocyte differentiation), along with cell cycle and subcellular localization processes. Some entries relate to neural/retinal context (visual perception and synapse localization), suggesting a broader role in signaling and differentiation across tissues. Overall, the cluster seems defined by growth/differentiation signaling rather than a single shared process.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043065","count":13},{"id":"GO:0008285","count":13},{"id":"GO:0010800","count":13},{"id":"GO:0060044","count":13},{"id":"GO:0030216","count":13}]},{"hash":"784587581566176059","title":"Ribosome Biogenesis and Translation Machinery","description":"This cluster centers on the protein synthesis machinery: translation and ribosome biogenesis/assembly, including rRNA processing. DNA damage\u2013related regulation terms may reflect stress-responsive control of translation, but the dominant theme is ribosome production and protein synthesis.","confidence":"High","size":19,"edges":165,"triangles":874,"max_degree":18,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":13},{"id":"GO:0042254","count":5},{"id":"GO:0042273","count":4},{"id":"GO:0000027","count":3},{"id":"GO:0000028","count":3}]},{"hash":"1663593927445007966","title":"Unknown","description":"The terms point to a highly heterogeneous mix of processes (cell cycle regulation, skin/keratinocyte development, renal transport, xenobiotic response, DNA-related processes, and metabolism), with several entries labeled obsolete. There isn't a single cohesive function or pathway that ties the cluster together, so a specific, representative label cannot be confidently assigned.","confidence":"","size":19,"edges":14,"triangles":2,"max_degree":5,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:2001153","count":5},{"id":"GO:0007568","count":5},{"id":"GO:0080111","count":5},{"id":"GO:1900087","count":5},{"id":"GO:0003335","count":5}]},{"hash":"1105174895846831621","title":"DNA-templated transcription and cell cycle signaling","description":"The top GO terms point to core transcriptional activity (DNA-templated transcription) and several cell-cycle related processes (mitotic centrosome separation; budding apical bud growth), suggesting a cluster of proteins involved in coordinating gene expression with cell division. Additional terms related to stress granule disassembly and signaling modulation (phosphorelay system, TGF-beta signaling) indicate broader signaling and RNA stress response roles that are linked to transcriptional control during growth. Overall, the proteins appear to function in transcription coupled to cell-cycle regulation with ancillary signaling and RNA stress responses, rather than a single precise pathway.","confidence":"Medium","size":19,"edges":27,"triangles":21,"max_degree":9,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0000160","count":2},{"id":"GO:0006470","count":2},{"id":"GO:0007118","count":2},{"id":"GO:0007100","count":2}]},{"hash":"563403490202956569","title":"Proteasome-Dependent Proteolysis in Meiosis and Development","description":"The top terms strongly point to ubiquitin-dependent protein degradation and SCF-proteasome pathways, implying regulated proteolysis. Co-occurring terms about spindle assembly in female meiosis, oocyte maturation, neural tube and ventricle development, and microtubule dynamics suggest this proteolytic activity is coordinated with meiosis and early embryogenesis. Together these indicate a cluster of proteins centered on proteostasis during cell division and development.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":8},{"id":"GO:0031146","count":7},{"id":"GO:0090073","count":5},{"id":"GO:0007057","count":5},{"id":"GO:0070544","count":5}]},{"hash":"383695510323702922","title":"Glycolysis and Fructose Metabolism","description":"The GO terms cluster around central carbohydrate metabolism, especially glycolysis, fructose processing, and pentose-phosphate pathway regulation, suggesting proteins in this cluster mainly participate in sugar processing for energy. A few terms (cobalt response, intestinal epithelial development) are outliers and do not change the core interpretation.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046835","count":3},{"id":"GO:0006000","count":2},{"id":"GO:0043456","count":2},{"id":"GO:1904024","count":2},{"id":"GO:0006003","count":2}]},{"hash":"1961727231034492947","title":"Membrane transport and secretion","description":"Top terms cluster around transport and secretion across membranes: bacteriocin transport and immunity; oligopeptide export; peptide pheromone export; protein secretion by the Type I secretion system; phospholipid and ceramide translocation; cysteine transport; and antigen processing via MHC class I, which aligns with peptide transport/processing. Some terms like response to mercury ion are stress-related but do not overturn the dominant transport/secretion theme.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043213","count":5},{"id":"GO:0030153","count":5},{"id":"GO:0090374","count":5},{"id":"GO:0099040","count":5},{"id":"GO:0000770","count":5}]},{"hash":"1692730848476568064","title":"Kinase signaling regulators and mitosis control","description":"This cluster centers on regulatory proteins that modulate kinase signaling and cell division: negative regulation of ERK/MAPK pathways and T cell receptor signaling, dephosphorylation of tyrosine residues, and regulation of protein kinase activity, along with mitotic processes such as spindle elongation and chromosome passenger complex localization. The presence of additional terms like mRNA capping suggests ancillary regulatory roles, but the dominant theme is signaling regulation linked to mitosis. ","confidence":"Medium","size":19,"edges":153,"triangles":816,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0000200","count":14},{"id":"GO:0035335","count":14},{"id":"GO:0070373","count":14},{"id":"GO:0050860","count":14},{"id":"GO:1902846","count":12}]},{"hash":"1701553448805742604","title":"Plant cell wall glycoprotein biosynthesis","description":"The cluster is dominated by plant-related cell wall and glycoprotein terms: root hair cell development; cell wall organization; arabinogalactan protein metabolism; mucilage biosynthesis; and poly-N-acetyllactosamine biosynthetic processes. These point to biosynthesis and modification of glycoproteins (notably AGPs) and polysaccharides that compose the plant cell wall and secreted mucilage, supporting root hair formation and cell-wall remodeling. A few terms (e.g., infection structure, insect visual primordium) are less congruent and may reflect broader or cross-kingdom annotations, but the overall theme is plant cell wall glycoprotein biosynthesis. ","confidence":"High","size":19,"edges":94,"triangles":179,"max_degree":15,"top_function":null,"top_go_terms":[{"id":"GO:0080147","count":6},{"id":"GO:0075015","count":5},{"id":"GO:0071555","count":4},{"id":"GO:0030311","count":4},{"id":"GO:0042248","count":4}]},{"hash":"586095096873236806","title":"Translational initiation and ribosome dynamics","description":"Predominant GO terms center on initiation, preinitiation complex formation, regulation of translation, ribosome disassembly, and maintenance of translational fidelity, suggesting a cohesive group of proteins involved in translation initiation and ribosome handling; a couple of outliers (dosage compensation and acyl-CoA metabolism) are minor, not breaking the overall theme.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032790","count":1},{"id":"GO:0002188","count":1},{"id":"GO:0002192","count":1},{"id":"GO:0009048","count":1},{"id":"GO:1990145","count":1}]},{"hash":"806551650761295446","title":"Mitochondrial gene expression and mitophagy","description":"The terms cluster around mitochondrial RNA processing and ribosome assembly, translation, and cellular respiration, with an additional note on mitophagy regulation. A chloroplast rRNA processing term appears but is outnumbered by mitochondrial-focused terms, supporting a theme of mitochondrial gene expression and quality control rather than chloroplast processes.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901259","count":1},{"id":"GO:0000963","count":1},{"id":"GO:0045333","count":1},{"id":"GO:1902775","count":1},{"id":"GO:0000463","count":1}]},{"hash":"1636951211928215194","title":"Neuroimmune TLR Signaling and Synapse Development","description":"The cluster shows enrichment for Toll-like receptor signaling pathways (TLR6, TLR8, TLR9) and microbial response terms, combined with neuronal development terms such as axonogenesis and synapse assembly, suggesting proteins involved in neuroimmune signaling and neural connectivity, possibly linking innate immune sensing to synaptic regulation.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0007409","count":3},{"id":"GO:0009620","count":2},{"id":"GO:0071726","count":2},{"id":"GO:0034162","count":2}]},{"hash":"2237139428946560624","title":"Actin-driven vesicle trafficking and cytokinesis","description":"This cluster centers on processes tied to the actin cytoskeleton, including vesicle transport along actin filaments, membrane addition during cytokinesis, and mitotic spindle orientation, indicating a collection of proteins involved in actin remodeling, vesicle trafficking, and cell division/morphogenesis. Additional terms touch on secretory granule localization and epithelial organization, suggesting a broader role in cytoskeleton\u2013secretion dynamics during cell migration and tissue development.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902405","count":3},{"id":"GO:0031585","count":3},{"id":"GO:0030050","count":3},{"id":"GO:0038089","count":3},{"id":"GO:0032252","count":3}]},{"hash":"944067330262857541","title":"Ion Transport and Membrane Excitability","description":"These proteins cluster around ion transport and membrane excitability, with GO terms emphasizing potassium and calcium transmembrane transport, calcium channels, and membrane depolarization in excitable cells like Purkinje fibers. While some terms touch sensory perception and inflammatory signaling, the core signal is ion movement across membranes governing electrical activity. ","confidence":"Medium","size":19,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":2},{"id":"GO:1903444","count":1},{"id":"GO:0061577","count":1},{"id":"GO:0060453","count":1},{"id":"GO:0051928","count":1}]},{"hash":"1238183642213458087","title":"Chloroplast PSII Assembly","description":"The dominant GO term is photosystem II assembly, pointing to chloroplast PSII complex formation; the other terms reference protein folding/assembly (tubulin) but PSII assembly remains the clearest, representative function for this cluster, even though there are no inferred interactions among proteins.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007023","count":1},{"id":"GO:0007021","count":1},{"id":"GO:0010207","count":1}]},{"hash":"2281966037235038727","title":"Chromatin organization and transcription regulation","description":"The top GO terms cluster around chromatin architecture and modification (heterochromatin formation, nucleosome-related processes, histone modifications) and regulation of transcription start site choice, with spindle assembly offering a tangential link to chromosome handling. Despite several obsolete terms, the coherent theme is chromatin structure influencing transcription. ","confidence":"Medium","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":2},{"id":"GO:0071441","count":1},{"id":"GO:0001178","count":1},{"id":"GO:0030491","count":1},{"id":"GO:0042766","count":1}]},{"hash":"1954895893008008378","title":"Developmental Morphogenesis and Cell Migration","description":"The top GO terms center on organ development and morphogenesis\u2014neural tube closure, corpus callosum development, and trachea formation\u2014along with cell migration, which is central to shaping tissues during development. A few other terms (immune signaling, virus response, metabolism, apoptosis) are present but seem secondary to the core developmental/migration theme. This suggests the cluster mainly groups proteins involved in developmental morphogenesis linked by cell movement.","confidence":"Medium","size":19,"edges":48,"triangles":33,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016477","count":19},{"id":"GO:0010898","count":19},{"id":"GO:0022038","count":19},{"id":"GO:0050853","count":19},{"id":"GO:0043065","count":19}]},{"hash":"525284611555574697","title":"LPS Core and Envelope Biosynthesis","description":"The cluster is dominated by GO terms for lipopolysaccharide biosynthesis, including core region and ADP-L-glycero-heptose biosynthetic processes, indicating proteins involved in constructing the bacterial LPS envelope. Other terms such as dephosphorylation and antibiotic response may reflect ancillary cellular processes or stress responses, but the main theme is LPS production.","confidence":"High","size":19,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":5},{"id":"GO:0055114","count":4},{"id":"GO:0070389","count":3},{"id":"GO:0016311","count":3},{"id":"GO:0009244","count":3}]},{"hash":"602737220378499668","title":"Amino acid biosynthesis and related metabolism","description":"The cluster centers on biosynthetic and metabolic processes involving amino acids (thiamine, threonine, tryptophan, methionine) and related pathways, with ancillary terms like carbohydrate phosphorylation and hydrogen peroxide biosynthesis. Some terms are obsolete or stress/hormone related, but the dominant signal is amino acid biosynthesis, suggesting the proteins function together in amino acid metabolism.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":4},{"id":"GO:0009086","count":3},{"id":"GO:0009088","count":3},{"id":"GO:0046835","count":3},{"id":"GO:0006569","count":3}]},{"hash":"404181875142304438","title":"Diverse Biosynthetic Pathways","description":"Proteins in this cluster are enriched for a variety of biosynthetic and metabolic processes spanning different organisms and pathways, including fatty acid elongation, mycolic acid and poly-hydroxybutyrate biosynthesis, retinal metabolism, acetoin catabolism, and tropane alkaloid biosynthesis, with an additional transcription regulation term. This points to a broad metabolic/biosynthetic theme rather than a single, cohesive pathway. A few terms (e.g., lung development) appear less clearly connected and may reflect annotation noise, but the overall signal supports a biosynthesis-focused cluster.","confidence":"Medium","size":19,"edges":96,"triangles":194,"max_degree":16,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":16},{"id":"GO:0030324","count":16},{"id":"GO:0045150","count":16},{"id":"GO:0042438","count":16},{"id":"GO:0071768","count":16}]},{"hash":"823658218841556227","title":"Fungal cell wall biosynthesis and glucan metabolism","description":"The top GO terms strongly point to fungal-type cell wall processes, including cell wall organization, beta-glucan biosynthesis and biogenesis, and glucan remodeling. Additional terms for fungal cell wall components and glycosylation support a cohesive theme around cell wall construction and modification, with oligosaccharide metabolism aligning to wall polysaccharides. Overall, these terms suggest a function centered on fungal cell wall biosynthesis/metabolism.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006076","count":2},{"id":"GO:0031505","count":2},{"id":"GO:0009718","count":2}]},{"hash":"1389787219494484602","title":"Unknown","description":"The cluster shows a mix of RNA processing (mRNA splicing via spliceosome, polyadenylation), DNA repair, various transport-related processes (bacteriocin and teichoic acid transport, xenobiotic export), and broad functions like phosphorylation, with no single coherent functional theme tying all proteins together.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0009405","count":2},{"id":"GO:0046618","count":1}]},{"hash":"292672455286850991","title":"Oxidative Stress Response and Redox Homeostasis","description":"This cluster centers on cellular redox balance and responses to oxidative stress, with multiple terms for redox homeostasis, oxidative stress response, and detoxification of oxidants. The inclusion of transcriptional regulation under RNA polymerase II and a prolyl hydroxylation term suggests coordination between redox status and transcriptional control or protein modification. Overall, the proteins appear to function together in managing oxidative stress and maintaining redox homeostasis.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":6},{"id":"GO:0000122","count":6},{"id":"GO:0045454","count":5},{"id":"GO:0033158","count":4},{"id":"GO:0034599","count":4}]},{"hash":"416815627307294849","title":"Cell growth and fate signaling","description":"The GO terms cluster around growth, cell cycle, and signaling pathways (including Wnt), with accompanying annotations for apoptosis and epithelial polarity, suggesting involvement in regulation of cell fate, proliferation, and tissue organization. Some terms like antibiotic biosynthetic process and obsolete oxidation-reduction term may reflect annotation noise rather than core biology in this cluster.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0016049","count":2},{"id":"GO:2000171","count":2},{"id":"GO:0007049","count":2}]},{"hash":"2188101248110499015","title":"Oxidative Stress Response and Detoxification","description":"The top GO terms converge on defense against oxidative damage and detoxification processes, including glutathione biosynthesis, responses to reactive oxygen species (hydrogen peroxide, superoxide), and arsenic-related detox, along with related protein turnover and ubiquitination regulation that can modulate stress responses. This combination suggests a cohesive cluster focused on redox homeostasis and detox pathways rather than a single specific pathway.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046938","count":1},{"id":"GO:0035729","count":1},{"id":"GO:2000490","count":1},{"id":"GO:2001237","count":1},{"id":"GO:0000303","count":1}]},{"hash":"1741942837860167238","title":"Immunoglobulin diversification and DNA repair","description":"The terms point to antibody gene diversification activities (somatic hypermutation, isotype switching, humoral response) alongside multiple DNA repair and replication processes (base-excision repair, nucleotide-excision repair, DNA replication, mitotic chromosome maintenance). This combination suggests a cluster of proteins coordinating immune diversification with genome maintenance in B cells.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045876","count":1},{"id":"GO:0045190","count":1},{"id":"GO:0006286","count":1},{"id":"GO:0002455","count":1},{"id":"GO:0006289","count":1}]},{"hash":"2034135043513139978","title":"Tetrapyrrole and chlorophyll biosynthesis","description":"The Top Terms center on heme and chlorophyll/tetrapyrrole biosynthesis (heme biosynthetic process, protoporphyrinogen IX biosynthesis, chlorophyll biosynthetic process), suggesting a core theme around tetrapyrrole metabolism. A few transport-related terms and mitochondrial assembly terms appear as context, but the prominent signal is tetrapyrrole production in plastids/mitochondria.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032981","count":1},{"id":"GO:0045600","count":1},{"id":"GO:0006730","count":1},{"id":"GO:0006783","count":1},{"id":"GO:0019353","count":1}]},{"hash":"2009389986398821562","title":"Nucleobase Transporters","description":"The top GO terms repeatedly point to transport of various nucleobases (adenine, guanine, hypoxanthine, uracil, xanthine, urate) across the plasma membrane, suggesting this cluster comprises nucleobase transport proteins. A couple of kinetochore-related terms appear but aren\u2019t representative of the dominant function.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035344","count":1},{"id":"GO:1903825","count":1},{"id":"GO:0098721","count":1},{"id":"GO:0015747","count":1},{"id":"GO:0098710","count":1}]},{"hash":"194071766479289063","title":"Unknown","description":"The Top Terms are scattered across cartilage development, kidney basement membrane development and filtration, hormone response (estradiol/estrous cycle), endocytosis, angiogenesis, and lipid catabolic processes. With no edges connecting proteins, there is no coherent single functional theme tying these terms together, so a general Unknown label is most appropriate.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0002063","count":4},{"id":"GO:0031953","count":3},{"id":"GO:0071392","count":3},{"id":"GO:0006898","count":3},{"id":"GO:0045765","count":3}]},{"hash":"1331686023099313302","title":"Unknown","description":"Unknown","confidence":"","size":19,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0052889","count":3},{"id":"GO:2000344","count":3},{"id":"GO:0007283","count":3},{"id":"GO:2000884","count":3},{"id":"GO:0016239","count":3}]},{"hash":"2068943472885217280","title":"Cardiac development and Notch signaling","description":"The Top Terms include cardiac right atrium morphogenesis, venous endothelial cell differentiation, and Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation, which together point to a cardiac development theme; other terms such as phosphate ion transport and mRNA processing appear but are less central, so the cluster is best described as a cardiac development/signaling group with Notch involvement.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":3},{"id":"GO:0006817","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0003213","count":2},{"id":"GO:0060843","count":2}]},{"hash":"2098805786415771399","title":"Neuro-immune signaling cluster","description":"This cluster shows GO terms spanning neural development and neurotransmitter response (corpus callosum development, axonogenesis, cellular response to dopamine) together with strong innate immune signals (lipopolysaccharide response, dsRNA response, defense against Gram-positive bacteria, interferon-beta production). The mixture suggests proteins involved in signaling pathways that integrate neural and immune stimulus responses rather than a single, cohesive function. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903351","count":3},{"id":"GO:0022038","count":3},{"id":"GO:0071222","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0045359","count":3}]},{"hash":"220030878765247039","title":"Ion and Sugar Transmembrane Transporters","description":"The GO terms are dominated by transmembrane transport activities for nitrite/nitrate, phosphate, sodium, galactose, and fucose, plus neurotransmitter loading into synaptic vesicles, pointing to a shared function in membrane transport. A couple of terms relate to transcription regulation and chromatin remodeling, which may reflect regulatory roles but are less central to the main theme. Thus, the cluster is best described as membrane transporters for ions and sugars.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0015707","count":1},{"id":"GO:0035435","count":1},{"id":"GO:0015706","count":1}]},{"hash":"684625368970021176","title":"Mitochondrial metabolism and protein turnover","description":"The terms show a strong mitochondrial signal: aerobic respiration and proton transmembrane transport point to energy production in mitochondria. Also, protein catabolic processes and ubiquitin recycling indicate protein turnover and quality control, which often accompany mitochondrial function. Some terms related to viral/symbiont interactions appear but do not dominate; overall the cluster aligns best with mitochondrial metabolism paired with protein degradation.","confidence":"Medium","size":19,"edges":4,"triangles":0,"max_degree":2,"top_function":"protein catabolic process","top_go_terms":[{"id":"GO:0009060","count":5},{"id":"GO:0016032","count":5},{"id":"GO:1902600","count":5},{"id":"GO:0006627","count":5},{"id":"GO:1901143","count":5}]},{"hash":"2120599040974902878","title":"Heart and vascular development via Notch signaling","description":"The GO terms point to embryonic development with a strong emphasis on heart morphogenesis and vascular differentiation (cardiac right atrium morphogenesis; Notch signaling in secondary heart field), plus venous endothelial differentiation and other development terms. A few metabolism-related terms are present but appear peripheral to the core cardiovascular development theme.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":2},{"id":"GO:0060528","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0060843","count":2},{"id":"GO:0003213","count":2}]},{"hash":"1596991846529328576","title":"Innate Immune Sensing and Antigen Presentation","description":"The top terms cluster around innate immune recognition and downstream antigen presentation: NLRP3 inflammasome complex assembly, TLR9 signaling, positive regulation of interferon-beta production, xenophagy, and MHC class I biosynthesis with dendritic cell antigen processing and presentation. Also, regulation of non-canonical NF-kappaB signaling and muramyl dipeptide response support pathogen detection and inflammatory signaling. Together these terms point to a cohesive theme of innate immune activation bridging to adaptive antigen presentation.","confidence":"High","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044546","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0034162","count":2},{"id":"GO:0045359","count":2},{"id":"GO:0046827","count":2}]},{"hash":"765171946810893988","title":"Bacterial metabolism: vitamins, lipids, xenobiotics","description":"The top GO terms cluster around biosynthesis of vitamins and lipids (biotin, menaquinone, antibiotic biosynthesis) as well as catabolic processes for various small molecules (triglycerides, uracil, 1,2-dichloroethane, beta-ketoadipate). This mix suggests a broad metabolic module handling diverse small-molecule synthesis and degradation, rather than a single precise pathway. ","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":7},{"id":"GO:0017000","count":7},{"id":"GO:0009234","count":7},{"id":"GO:2000124","count":6},{"id":"GO:0019433","count":6}]},{"hash":"1872950650947108600","title":"Endosomal trafficking and receptor recycling regulators","description":"These proteins show strong representation for endocytic processes, with GO terms like receptor recycling and regulation of endosome size. While there are some mixed annotations (e.g., synaptic transmission, signaling pathways), the core pattern points to endosome-associated regulation of membrane receptors, suggesting a cluster of endosomal trafficking regulators.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001881","count":1},{"id":"GO:0051036","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0035249","count":1},{"id":"GO:0006355","count":1}]},{"hash":"184311975348560485","title":"Ubiquitin-Dependent Signaling Regulators","description":"The prominent GO terms are protein ubiquitination and ubiquitin-dependent proteolysis, with additional references to NF-kappaB/NFAT signaling regulation and inflammatory processes. The presence of these ubiquitin-related and signaling terms suggests these proteins function as regulators within ubiquitin-mediated signaling pathways, rather than representing a single specific function, justifying a label focused on ubiquitin-dependent signaling control.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0051534","count":2},{"id":"GO:0006511","count":2},{"id":"GO:0086070","count":2},{"id":"GO:1903444","count":2}]},{"hash":"250840801699559889","title":"Neuronal development and innate immune signaling","description":"The cluster highlights neural development processes (axonogenesis, synapse assembly) together with innate immune responses (TLR signaling, response to fungus, diacyl lipopeptide) and dopamine-related signaling, suggesting proteins that participate in neuroimmune communication and signaling modulation. The mix of neural and immune GO terms, plus signaling regulation terms, supports a theme of neuroimmune cross-talk rather than a single isolated function.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0007409","count":5},{"id":"GO:0006469","count":5},{"id":"GO:0071260","count":5},{"id":"GO:0009620","count":4},{"id":"GO:0071726","count":4}]},{"hash":"2022904753732136179","title":"Unknown","description":"The top GO terms span antibiotic response, ncRNA-mediated silencing, various transport and lipid/biosynthesis processes, and DNA repair, with no single cohesive function linking the proteins. This heterogeneity suggests no clear shared biological role for the cluster.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0010372","count":1},{"id":"GO:0031047","count":1},{"id":"GO:1902475","count":1},{"id":"GO:0008152","count":1}]},{"hash":"810446137045628246","title":"Unknown","description":"The GO terms are highly diverse (heart development, IgA isotype switching, transcription regulation, cocaine response, and various histone modification terms, many labeled obsolete), and there are no connecting functional threads or interactions among the proteins (Edges: 0, Max Degree: 0). This dispersion makes it impossible to assign a coherent, representative function to the cluster.","confidence":"","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090309","count":1},{"id":"GO:0045605","count":1},{"id":"GO:0034772","count":1},{"id":"GO:0007507","count":1},{"id":"GO:0048298","count":1}]},{"hash":"678292113015769065","title":"Innate Immune Activation and Antibacterial Defense","description":"This cluster is dominated by terms tied to innate immunity and antibacterial responses, such as innate immune response, defense against Gram-positive bacteria, LPS signaling, interferon-beta production, and xenophagy, pointing to immune activation and autophagic defense. A few terms (pollen recognition, glucocorticoid response, muscle differentiation) are less directly related but do not override the central theme.","confidence":"Medium","size":19,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":2},{"id":"GO:0050830","count":2},{"id":"GO:1904417","count":2},{"id":"GO:0045359","count":2},{"id":"GO:0031663","count":2}]},{"hash":"1618544902343378987","title":"Nucleotide biosynthesis and protein phosphorylation","description":"The cluster includes direct nucleotide biosynthesis processes (CTP biosynthetic process; dGTP biosynthetic process from dGDP; CDP phosphorylation) and protein autophosphorylation, pointing to a core theme of nucleotide metabolism linked to phosphorylation signaling. While several terms are less specific or obsolete, the strongest signals are nucleotide biosynthesis and kinase-related activity, with accompanying metabolic regulation cues such as redox homeostasis and fatty acid response. ","confidence":"Medium","size":18,"edges":110,"triangles":401,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0051259","count":3},{"id":"GO:0045454","count":3},{"id":"GO:0006186","count":2},{"id":"GO:0045920","count":2},{"id":"GO:0060416","count":2}]},{"hash":"836619258887279615","title":"RNA pseudouridylation and splicing","description":"The cluster is dominated by GO terms for RNA modification via pseudouridylation (snRNA, tRNA, mRNA) and spliceosomal complex assembly, pointing to a cohesive role in RNA processing and maturation. Other terms about transcription regulation and stress responses are present but secondary to the RNA processing theme.","confidence":"Medium","size":18,"edges":6,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":2},{"id":"GO:0000245","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0031120","count":2}]},{"hash":"834546007498685562","title":"Cardiac Calcium Signaling and Ion Transport","description":"The cluster is enriched for calcium-related processes (calcium ion transport, regulation of calcium transport, and membrane depolarization in Purkinje myocytes) and a cardiac hypertrophy term, suggesting a cohesive theme around calcium signaling and electrical activity in heart muscle. Other terms (manganese transport, gastric acid secretion, brown fat differentiation) are present but appear less central to this core function, possibly reflecting broader ion transport roles or secondary associations.","confidence":"Medium","size":18,"edges":23,"triangles":7,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":6},{"id":"GO:1903244","count":5},{"id":"GO:0051260","count":5},{"id":"GO:0097274","count":4},{"id":"GO:1903444","count":4}]},{"hash":"233942204255248505","title":"DNA replication and cell cycle regulation","description":"The cluster\u2019s top GO terms cluster tightly around DNA replication, mitotic/cell cycle processes, centrosome cycle, and DNA recombination, with supporting signals from transcription regulation. This points to a coherent functional theme centered on genome replication and cell division, with development-related terms possibly reflecting pleiotropy or broader regulatory roles. Confidence in this interpretation is Moderate.","confidence":"Medium","size":18,"edges":18,"triangles":6,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0045944","count":6},{"id":"GO:0048701","count":6},{"id":"GO:0000278","count":6},{"id":"GO:0007049","count":5}]},{"hash":"1575277052159806149","title":"Steroid and Retinoid Metabolism","description":"The cluster centers on hormone and vitamin A-related metabolism, with strong representation for androgen and testosterone biosynthesis, retinol/retinal metabolism, and bile acid production, plus supporting redox and xenobiotic response terms. This suggests a cohesive theme around lipid/sterol and retinoid metabolic pathways, hence the label.","confidence":"Medium","size":18,"edges":136,"triangles":607,"max_degree":17,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":15},{"id":"GO:0008209","count":14},{"id":"GO:0042574","count":14},{"id":"GO:0061370","count":14},{"id":"GO:0042572","count":14}]},{"hash":"1370241540194390763","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031126","count":2},{"id":"GO:0001015","count":2},{"id":"GO:0032968","count":2},{"id":"GO:0010964","count":2},{"id":"GO:2001173","count":2}]},{"hash":"51237675068747542","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006417","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0000470","count":1},{"id":"GO:0000963","count":1},{"id":"GO:0045333","count":1}]},{"hash":"2234759301324722983","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051607","count":1},{"id":"GO:0036292","count":1},{"id":"GO:0061321","count":1},{"id":"GO:0090305","count":1},{"id":"GO:0097500","count":1}]},{"hash":"66976043802277598","title":"Bacterial Growth, Capsule Biosynthesis, and Stress Response","description":"The top terms include DNA replication and cell division (growth/cell cycle) alongside capsule polysaccharide biosynthesis and cell wall organization (envelope features), plus glycolytic metabolism and stress-related responses (response to xenobiotic stimulus, response to cold). This suggests a cohesive bacterial growth and envelope biosynthesis module that also engages metabolic activity and environmental stress responses, rather than unrelated processes. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0071555","count":2}]},{"hash":"1908981511770134596","title":"Developmental transcriptional regulation","description":"This cluster centers on transcription-related processes (DNA-templated transcription and transcription regulation by RNA Pol II) and includes several developmentally focused terms across tissues (neural development, neuron projection extension, cerebral cortex development, bile duct development, and sperm capacitation), suggesting proteins that coordinate gene expression during development.  ","confidence":"Medium","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":3},{"id":"GO:0043046","count":2},{"id":"GO:0045793","count":2},{"id":"GO:0051573","count":2},{"id":"GO:0006915","count":2}]},{"hash":"1518722149965394058","title":"Vesicle trafficking and endocytosis","description":"The majority of GO terms point to vesicle formation, clathrin-dependent endocytosis, intracellular protein transport, and synaptic vesicle coating, with support from related processes such as platelet granule release and membrane lipid signaling; translation appears as an outlier. Overall, a common theme around vesicle trafficking and endocytosis emerges, hence this label.","confidence":"Medium","size":18,"edges":58,"triangles":79,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0072583","count":1},{"id":"GO:0006886","count":1},{"id":"GO:0016183","count":1},{"id":"GO:0070527","count":1}]},{"hash":"602692201449496033","title":"Wnt signaling and gonadal development","description":"Top GO terms indicate a core theme around the Wnt signaling pathway with associated gonadal and sex-hormone metabolism processes (e.g., estrogen and androgen metabolism, female gonad development). While other terms suggest broader stress or nuclear localization roles, the strongest signal is coupling of Wnt signaling to gonadal development. Confidence: Medium","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":3},{"id":"GO:1990166","count":2},{"id":"GO:0008209","count":2},{"id":"GO:0008210","count":2},{"id":"GO:1904646","count":2}]},{"hash":"692528338114114698","title":"Retina Development and Neural Signaling","description":"Several top GO terms point to retina-related processes (visual perception and retina vasculature development) alongside neural signaling (cell surface receptor signaling pathway, Notch regulation) and neural cell junction formation (paranodal and septate junction assembly). This pattern suggests proteins in the cluster participate in retinal development with associated signaling and junction organization, supporting the label \u201cRetina Development and Neural Signaling.\u201d","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":2},{"id":"GO:0046813","count":1},{"id":"GO:0031623","count":1},{"id":"GO:0090528","count":1},{"id":"GO:0030913","count":1}]},{"hash":"1778198878154387425","title":"Membrane Transport and ER Protein Folding","description":"This cluster is driven by transmembrane transport terms (phosphate ion and xenobiotic transport) and protein folding in the endoplasmic reticulum, suggesting a link between membrane transport activity and ER protein quality control. The presence of heat-stress related terms and regulation of heat response supports a role in stress-related protein handling, while other terms like DNA-templated transcription and replication may reflect broader cellular housekeeping or shared components. Overall, there\u2019s a coherent theme around membrane transport complemented by ER-associated folding/quality control and stress responsiveness, with some ancillary functions.","confidence":"Medium","size":18,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":3},{"id":"GO:0006855","count":3},{"id":"GO:0006351","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0006260","count":2}]},{"hash":"1513690301381134803","title":"Multi-Organ Development","description":"The Top Terms cluster around broad developmental processes affecting multiple organs and tissues (pituitary gland development, heart development, forebrain development, peripheral nervous system neuron development, subpallium development, digestive tract morphogenesis, gonad development). Although there are some oxidative-reduction terms, the dominant signal is organogenesis across diverse tissues, justifying a multi-organ development label.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021983","count":4},{"id":"GO:0055114","count":4},{"id":"GO:0098869","count":3},{"id":"GO:1902723","count":3},{"id":"GO:0007507","count":3}]},{"hash":"1153075078837611490","title":"Organogenesis and Tissue Morphogenesis","description":"The top GO terms cluster around development and morphogenesis across multiple organs (eye morphogenesis, lateral ventricle development, proximal tubule development) and developmental signaling (retinoic acid response, actin cytoskeleton polarity). Although some terms reflect broader cellular processes, the recurring theme is organogenesis and tissue shaping, suggesting these proteins collectively participate in developmental morphogenesis rather than a single, narrow function.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021670","count":3},{"id":"GO:0016310","count":2},{"id":"GO:0072014","count":2},{"id":"GO:0015840","count":2},{"id":"GO:0071474","count":2}]},{"hash":"404606528735282846","title":"Cardiovascular development and heart muscle signaling","description":"The top GO terms point to heart development, blood vessel morphogenesis, cardiac muscle hypertrophy, and regulation of muscle contraction, suggesting a cohesive theme around cardiovascular development and heart muscle function. Some terms ( xenobiotic response, synaptic potentiation) appear less central to this core theme.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0001569","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0035690","count":3}]},{"hash":"2110421045695291499","title":"Unknown","description":"The Top Terms cover diverse processes (DNA replication, cell-cycle transitions, kinetochore localization, and Hippo signaling) alongside neural signaling (excitatory postsynaptic potential, response to cocaine), skin differentiation, and cardiac proliferation, with no single clear function tying the cluster together. Confidence: None","confidence":"","size":18,"edges":36,"triangles":29,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046827","count":9},{"id":"GO:0006260","count":8},{"id":"GO:0060044","count":7},{"id":"GO:0030216","count":7},{"id":"GO:0035329","count":7}]},{"hash":"328390537155866710","title":"Embryonic skeletal and CNS development","description":"The cluster shows strong enrichment for embryonic morphogenesis and skeletal system development (cranial skeleton morphogenesis, skeletal system development) with neural-associated development terms (retina vasculature development, corpus callosum development) and mesenchymal tissue development, suggesting a shared embryonic development program across skeletal and nervous system lineages. DNA replication and transcription terms likely reflect proliferative states in developing tissues, but the dominant signal points to embryonic tissue morphogenesis in skeletal and neural contexts.","confidence":"Medium","size":18,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048701","count":10},{"id":"GO:0006260","count":10},{"id":"GO:0001501","count":8},{"id":"GO:0006351","count":8},{"id":"GO:0051965","count":7}]},{"hash":"1854660547749168492","title":"Neural signaling and cardiovascular development","description":"The cluster shows enrichment for nervous system signaling (excitatory postsynaptic potential, myelination) alongside cardiovascular development terms (branching in blood vessel morphogenesis, heart development, regulation of heart rate), suggesting proteins involved in signaling pathways that span neural and heart development.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060079","count":3},{"id":"GO:0006470","count":3},{"id":"GO:0001569","count":2},{"id":"GO:0022011","count":2},{"id":"GO:0007507","count":2}]},{"hash":"1875663784049505615","title":"Bacterial cell wall polysaccharide biosynthesis and glycosylation","description":"This cluster is enriched for GO terms related to cell wall biosynthesis and polysaccharide assembly (cell wall organization, teichoic acid, cellulose, hyaluronan biosynthesis, UDP-glucose metabolism) and for protein glycosylation pathways (O-linked glycosylation via GalNAc, Ser/Thr sites). The combination points to enzymes and processes involved in constructing bacterial surface polysaccharides and their glycosylation, typical of cell-wall-associated pathways. ","confidence":"High","size":18,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0036108","count":2},{"id":"GO:0030213","count":2},{"id":"GO:0030244","count":2},{"id":"GO:0006011","count":2}]},{"hash":"2214275416650908032","title":"Vacuolar amino acid transport under nutrient starvation","description":"The top GO terms point to transport of multiple amino acids (proline, asparagine, lysine, histidine) into the vacuole and cellular responses to nutrient stress (nitrogen and potassium starvation, acidic pH). This suggests a cohesive function: proteins involved in vacuolar import of amino acids during nutrient limitation. Some terms (vacuole fusion non-autophagic and certain transcription regulation terms) are less central or obsolete, but the dominant signal is vacuolar amino acid transport in nutrient-restricted conditions.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042144","count":2},{"id":"GO:0045944","count":2},{"id":"GO:1901481","count":2},{"id":"GO:0015824","count":2},{"id":"GO:0051365","count":2}]},{"hash":"642285362951075117","title":"Nutrient Transport and Metabolism","description":"The cluster collects proteins annotated with ammonium, methylammonium, and transepithelial ammonium transport, along with other nutrient-transport and metabolism terms (carbon dioxide transport, lipid metabolism, nitrogen utilization, iron homeostasis) and growth responses to nutrient limitation. This mix points to a general theme of nutrient uptake and metabolic regulation rather than a single, specific pathway, so the label \u201cNutrient Transport and Metabolism\u201d captures the common function across the cluster.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006629","count":2},{"id":"GO:0007124","count":1},{"id":"GO:0072488","count":1},{"id":"GO:0015670","count":1},{"id":"GO:0080181","count":1}]},{"hash":"1395807890003023172","title":"Lipid biosynthesis and adipocyte differentiation","description":"Top GO terms indicate sphingolipid and fatty acid biosynthesis and adipocyte differentiation, suggesting the cluster centers on lipid metabolism and fat cell development, despite some obsolete terms. This makes the label a concise representation of the dominant theme.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0006667","count":1},{"id":"GO:0050872","count":1},{"id":"GO:0010205","count":1},{"id":"GO:0070542","count":1}]},{"hash":"523456208551141831","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":4},{"id":"GO:0016266","count":2},{"id":"GO:0010306","count":2},{"id":"GO:0080147","count":2},{"id":"GO:0033621","count":1}]},{"hash":"1502426353716470074","title":"Unknown","description":"The top GO terms span neural development (corpus callosum development, neural tube closure) and development-related processes like cell migration, plus cell cycle/centrosome activity, immune signaling (B cell receptor signaling), and various stress/metabolic responses. This broad mix covers neural development and immune/metabolic signaling but lacks a single cohesive function that ties the cluster together, so no clear label beyond Unknown is justified.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0010571","count":6},{"id":"GO:0007098","count":6},{"id":"GO:0016477","count":5},{"id":"GO:0010898","count":5},{"id":"GO:0022038","count":5}]},{"hash":"443627447311258049","title":"Endosome-to-lysosome trafficking and autophagy","description":"The prominent GO terms center on intracellular vesicle transport toward lysosomes and autophagic processes, including endosome-to-lysosome transport, phagosome-lysosome fusion, autophagosome maturation, vesicle tethering/fusion, Golgi-to-endosome transport, and SNARE complex regulation. This points to a cohesive theme of vesicle trafficking and lysosome-related degradation pathways, with a minor note that a couple developmental terms may be incidental background signals.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008333","count":2},{"id":"GO:0090385","count":2},{"id":"GO:0045992","count":2},{"id":"GO:0097352","count":2},{"id":"GO:0099022","count":2}]},{"hash":"356398594733263982","title":"Unknown","description":"The top GO terms are diverse (hypoxia response, kinase activity regulation, mRNA transport, mitotic cell cycle, autophosphorylation, GTPase activity) and include several distinct membrane transport processes (calcium, amino acids, xenobiotics) and glycosphingolipid biosynthesis. With no edges connecting the proteins, there is no cohesive, single function tying the cluster together, so a unified label cannot be assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071456","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0031954","count":2}]},{"hash":"109999532784988276","title":"Cofactor biosynthesis and RNA methylation","description":"This cluster shows a strong representation of vitamin/cofactor biosynthesis (cobalamin, biotin, vitamin E) alongside RNA modification processes (7-methylguanosine capping and guanine-N7 methylation), suggesting a theme centered on metabolic cofactor production and RNA methylation. There are also xenobiotic/stress-response terms (response to xenobiotic stimulus, cocaine, tumor cell), which may reflect broader regulatory responses but do not override the primary signal. The lack of edges indicates the proteins may be functionally diverse or not tightly connected in this dataset, so the name captures the main cohesive theme with some caution.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":9},{"id":"GO:0006370","count":6},{"id":"GO:0035690","count":6},{"id":"GO:0009102","count":6},{"id":"GO:0010189","count":6}]},{"hash":"1486693928896628481","title":"Toll-like Receptor Signaling and Inflammation","description":"The top GO terms cluster around multiple TLR pathways (TLR4, TLR9, TLR10) and adapters (MyD88), with outputs including interferon-\u03b2 production, dendritic cell cytokine regulation, IL-18 production, macrophage activation, and an inflammatory response, indicating a cohesive innate immune signaling module.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034162","count":2},{"id":"GO:0045359","count":2},{"id":"GO:0002730","count":2},{"id":"GO:0032741","count":2},{"id":"GO:0042116","count":2}]},{"hash":"1216556097906035395","title":"Plant Hormone Response and Chromatin Regulation","description":"The terms point to plant hormone signaling (gibberellin and abscisic acid) coupled with chromatin/ genome organization activities (heterochromatin formation, telomere localization), and DNA repair, suggesting a cluster of hormone-responsive chromatin dynamics. Some terms (viral process, snRNA transcription) may be ancillary, but the dominant theme appears to be hormone signaling linked to chromatin-related functions.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0009739","count":3},{"id":"GO:1900033","count":3},{"id":"GO:1990414","count":3},{"id":"GO:1905778","count":3},{"id":"GO:0016032","count":3}]},{"hash":"1550273102173356090","title":"Neural development and synaptic signaling","description":"The top GO terms emphasize nervous system and hippocampus development, dendrite morphogenesis, and calcium-dependent exocytosis, which together point to neuronal development and synaptic function. While cell cycle and DNA replication terms appear, the dominant signal is neural development with synaptic signaling. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045956","count":10},{"id":"GO:0033138","count":10},{"id":"GO:0021766","count":10},{"id":"GO:0000278","count":10},{"id":"GO:0031647","count":10}]},{"hash":"1511298157640754345","title":"Unknown","description":"The top GO terms span diverse areas: neural development regulation, organ development (liver, renal), glycan processing, lipid metabolism (ceramide, sphinganine, fatty acids), fat cell differentiation, and photoinhibition, with no single dominant function or pathway tying them together. The cluster also has no edges, suggesting a lack of cohesive functional connectivity. Therefore, Unknown with None. ","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010977","count":1},{"id":"GO:0006491","count":1},{"id":"GO:0001889","count":1},{"id":"GO:0072001","count":1},{"id":"GO:0007053","count":1}]},{"hash":"2027137822859770506","title":"Unknown","description":"The GO terms cover disparate processes (vitamin and pigment biosynthesis, cell wall biosynthesis, metal cofactor assembly, unfolded protein response, ER stress regulation, DNA replication) with no single shared function or pathway, and there are no edges linking proteins, so there is no cohesive label to assign.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":1},{"id":"GO:0015995","count":1},{"id":"GO:0070389","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0070880","count":1}]},{"hash":"1757456881412925315","title":"Cell-cycle and apoptosis regulatory proteins","description":"These proteins are enriched for GO terms that regulate key cellular processes, notably the cell cycle (mitotic G2 DNA damage checkpoint signaling), transcription regulation by RNA polymerase II, and negative regulation of apoptosis and necroptosis, as well as ubiquitination. The presence of Toll-like receptor signaling regulation suggests immune stress responsiveness, but the strongest cluster signal centers on controlling progression, transcriptional activity, and cell survival. There are no observed edges, which is consistent with a set of regulators rather than a cohesive complex.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":2},{"id":"GO:0034121","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0043066","count":2},{"id":"GO:0000209","count":2}]},{"hash":"1741714827104473338","title":"Innate Immune Sensing and Antigen Presentation","description":"This cluster centers on innate immune recognition (TLR9 signaling, muramyl dipeptide response), inflammasome assembly (NLRP3), and regulation of interferon-\u03b2 production, alongside processes related to MHC class I biosynthesis, dendritic cell cytokine regulation, and xenophagy. The GO terms collectively point to a module of pathogen sensing, inflammatory signaling, and antigen processing/presentation, supporting a label around innate immunity and antigen presentation.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045359","count":2},{"id":"GO:0034162","count":2},{"id":"GO:0044546","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0046827","count":2}]},{"hash":"2277081050779341868","title":"Unknown","description":"The terms include centromere/mitosis-related functions (CENP-A chromatin assembly; chromosome passenger complex localization to spindle midzone) alongside immune and neuronal signaling terms (B cell receptor signaling; regulation of synaptic vesicle endocytosis), ubiquitination, and ion transport\u2014no single cohesive theme emerges.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090073","count":1},{"id":"GO:0034080","count":1},{"id":"GO:0034766","count":1},{"id":"GO:2000774","count":1},{"id":"GO:0044030","count":1}]},{"hash":"50339173657205515","title":"Innate Immune Signaling and Xenophagy","description":"This cluster centers on innate immune activation and pathogen sensing, featuring TLR9 signaling, NLRP3 inflammasome assembly, interferon-beta production, muramyl dipeptide response, and regulation of NF-\u03baB and MHC I biosynthesis, with links to xenophagy and ubiquitin-proteasome processes, indicating a cohesive module for inflammatory responses and autophagic clearance of pathogens.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":3},{"id":"GO:0045359","count":2},{"id":"GO:0034162","count":2},{"id":"GO:0044546","count":2},{"id":"GO:0031146","count":2}]},{"hash":"811974410449439335","title":"Chromatin regulation and transcriptional control","description":"This cluster is enriched for DNA-templated transcription and histone methylation, indicating chromatin-level regulation of gene expression. Additional terms for mRNA transport, mitotic cell cycle, kinase activity regulation, autophosphorylation, and actin nucleation suggest coordinated signaling and cellular processes linked to transcriptional control and cell division. Overall, the dominant theme points to chromatin-mediated transcription regulation with related cell-cycle and signaling functions.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0051568","count":3},{"id":"GO:0071456","count":3},{"id":"GO:0071902","count":3},{"id":"GO:0034729","count":3}]},{"hash":"2106745788904060628","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0071222","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0018401","count":2},{"id":"GO:0055114","count":2}]},{"hash":"833644134965676713","title":"Unknown","description":"Unknown","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903265","count":2},{"id":"GO:0061158","count":2},{"id":"GO:0010586","count":2},{"id":"GO:1903886","count":2},{"id":"GO:0035278","count":2}]},{"hash":"45280515553533736","title":"Unknown","description":"The top GO terms span markedly different processes, including leukotriene biosynthesis, development, an ERAD pathway, various chromosome condensation/segregation steps, general cell division, morphogenesis, and even tRNA gene clustering, offering no single cohesive function to label the cluster with confidence.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019370","count":2},{"id":"GO:0007275","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0010032","count":1},{"id":"GO:0051306","count":1}]},{"hash":"1216963008583832757","title":"Nucleic Acid Replication and Organelle RNA Processing","description":"The cluster includes several GO terms tied to DNA replication and DNA damage checkpoints, as well as DNA repair, suggesting a core theme of nucleic acid maintenance. It also features organelle RNA processing (chloroplast and mitochondrial) and mitochondrial ribosomal assembly, pointing to organelle gene expression. Some outliers (e.g., immune-related regulation) may reflect annotation noise, but the dominant signal supports genome maintenance and organelle RNA biology.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:1901259","count":1},{"id":"GO:0000963","count":1},{"id":"GO:0045333","count":1},{"id":"GO:1902775","count":1}]},{"hash":"1144078964379013310","title":"Virus\u2013host interaction and viral life cycle","description":"The top GO terms cluster around viral processes\u2014virion assembly, viral life cycle, proviral latency, host-mediated activation of viral replication, and viral release\u2014pointing to a cohesive theme of virus-host interactions and stages of the viral life cycle. A few outliers (e.g., protein folding, sepal formation) are present but do not outweigh the dominant viral signal. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000276","count":1},{"id":"GO:0019068","count":1},{"id":"GO:0048453","count":1},{"id":"GO:0075713","count":1},{"id":"GO:0006457","count":1}]},{"hash":"726228943890912405","title":"Plant hormone biosynthesis and fruit ripening","description":"This cluster is dominated by GO terms on plant hormone biosynthesis (ethylene, gibberellin, auxin, salicylic acid) and fruit ripening, along with related secondary metabolite biosynthesis (proanthocyanidins) and stress-related responses like hydrogen peroxide\u2013mediated PCD. A few terms (e.g., penicillin biosynthesis) appear unrelated, but the overall theme points to hormone-driven metabolism and fruit development rather than a single non-hormonal pathway.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009693","count":2},{"id":"GO:0009835","count":2},{"id":"GO:0046244","count":2},{"id":"GO:0042318","count":2}]},{"hash":"631628908740538761","title":"Regulation of cell proliferation and mitosis","description":"This cluster\u2019s top GO terms are dominated by processes tied to cell growth and division, including positive regulation of cell population proliferation, mitotic cell cycle, and mitotic spindle assembly. Supporting themes include RNA guanine-N7-methylation and polyamine biosynthetic process, which relate to RNA processing and biosynthesis needed for cell division, as well as ubiquitin-related pathways reflecting protein turnover during the cell cycle. Viral process and cytokine production appear only modestly, suggesting the core theme is regulation of proliferation and mitosis rather than immune or viral responses. ","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0000183","count":2},{"id":"GO:0006596","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0008284","count":2}]},{"hash":"1211479184075619505","title":"Developmental and cellular regulation","description":"This cluster links to diverse regulatory roles: developmental processes (forebrain development, skeletal morphogenesis), epigenetic control (histone H3-K27 methylation), protein turnover (ubiquitination and SCF proteasomal degradation), signaling and cell-cycle modulation, mRNA splicing, and actin dynamics. The shared theme is broad regulatory function rather than a single pathway, so a high-level name reflecting development and cellular regulation fits best.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061087","count":3},{"id":"GO:0048705","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0070317","count":2},{"id":"GO:0030900","count":2}]},{"hash":"225212032993294206","title":"Innate Immune Sensing and Antigen Presentation","description":"The top GO terms cluster around innate immune detection and downstream antigen presentation: NLRP3 inflammasome assembly, TLR9 signaling, positive regulation of interferon-\u03b2 production, xenophagy, and positive regulation of MHC class I biosynthesis and dendritic cell antigen processing/presentation, along with proteasomal protein catabolic processes linked to antigen generation. This pattern suggests a coherent module of proteins coordinating pathogen sensing, inflammatory signaling, and presentation of antigens to T cells.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046827","count":2},{"id":"GO:0044546","count":1},{"id":"GO:0031146","count":1},{"id":"GO:0034162","count":1},{"id":"GO:0045359","count":1}]},{"hash":"248025076601055083","title":"Epigenetic Regulation and Transcription","description":"The top GO terms are dominated by regulation of transcription by RNA polymerase II and chromatin-related modifications (histone acetylation/methylation and DNA methylation\u2013dependent heterochromatin). While a few terms touch on trafficking or development, the core signal across the cluster points to epigenetic control of gene expression.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043001","count":2},{"id":"GO:0007399","count":2},{"id":"GO:0046909","count":2},{"id":"GO:0090309","count":1},{"id":"GO:0045605","count":1}]},{"hash":"1205212705126179802","title":"ER Stress Response and Protein Folding","description":"Most of the enriched GO terms describe processes in the endoplasmic reticulum, including protein folding (ER), response to ER stress, and detoxification of reactive species, indicating ER quality-control and redox homeostasis. The presence of prolyl hydroxylation suggests maturation steps for secreted/ER-targeted proteins. A couple of transcription regulation terms appear but are not central to this cluster. Overall, the dominant theme is ER-associated protein handling and oxidative stress responses.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0033158","count":1},{"id":"GO:0034599","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0055114","count":1}]},{"hash":"1195257372976161319","title":"Membrane Transporters and Mitochondrial Homeostasis","description":"The proteins are enriched for transmembrane transport of nutrients and ions (glucose, pantothenate, biotin, myo-inositol, sodium export), plus links to glutathione metabolism and regulation of mitochondrial membrane potential and oxidative-stress responses. This suggests a coherent membrane transport and cellular energy/redox homeostasis module.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904659","count":2},{"id":"GO:0015887","count":2},{"id":"GO:0008292","count":2},{"id":"GO:0015878","count":2},{"id":"GO:0015798","count":2}]},{"hash":"2002141559261600633","title":"Embryonic and Tissue Development","description":"The top GO terms cluster around development across multiple tissues (skeletal morphogenesis, forebrain and spinal cord development, multicellular organism development) with supporting terms like pigmentation and epithelial differentiation, plus VEGF-related responses. This suggests proteins broadly involved in ontogeny rather than a single pathway, hence a Development label is appropriate despite no observed interactions in the cluster.","confidence":"High","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048705","count":2},{"id":"GO:0030900","count":2},{"id":"GO:0060528","count":2},{"id":"GO:0007018","count":2},{"id":"GO:0043473","count":2}]},{"hash":"339546817234433188","title":"Innate antimicrobial defense against fungi and bacteria","description":"Most top GO terms point to innate immune responses to pathogens, especially fungi and Gram-positive bacteria, with interleukin-1 beta production and neutrophil-mediated antifungal activity. While some terms (fibrinolysis, glucose stimulus response, midbrain development) are less directly linked, the dominant theme across the cluster is antimicrobial innate defense and inflammatory signaling.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050720","count":2},{"id":"GO:0050832","count":2},{"id":"GO:0070947","count":2},{"id":"GO:2000097","count":2},{"id":"GO:0042730","count":2}]},{"hash":"233298831855526932","title":"Unknown","description":"The top GO terms span a mix of biosynthetic processes, hormone signaling, detoxification, and even DNA repair, across potentially different species, with no single unifying function tying the proteins together. The lack of edges and the diverse functional themes suggest there is no coherent cluster function to label beyond Unknown.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0009736","count":3},{"id":"GO:2000124","count":3},{"id":"GO:0019433","count":3}]},{"hash":"887857787488914833","title":"Unknown","description":"The listed GO terms are disparate (obsolete redox process, iron ion response, folate transport, and methotrexate transport) with no evident shared function or interaction pattern among the 18 proteins, so a coherent, specific cluster name cannot be assigned.","confidence":"","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0010039","count":1},{"id":"GO:0015885","count":1},{"id":"GO:0051958","count":1}]},{"hash":"644472745606437343","title":"ER organization and stress response","description":"This cluster is dominated by GO terms related to endoplasmic reticulum organization and ER stress response, including ER tubular network organization, ER inheritance, and response to ER stress; it also touches on nuclear pore complex assembly and mitotic nuclear membrane reassembly, reflecting ER\u2013nuclear envelope dynamics. A couple of terms (kidney development, bitter taste) appear as unlikely or off-target annotations.","confidence":"Medium","size":18,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010043","count":2},{"id":"GO:0001822","count":2},{"id":"GO:0030206","count":2},{"id":"GO:0051292","count":1},{"id":"GO:0071786","count":1}]},{"hash":"305900490167421606","title":"Ubiquitination-Driven Proteasomal Degradation","description":"The top GO terms are dominated by ubiquitination and proteasome-related processes (autoubiquitination, SCF-dependent proteasomal degradation, polyubiquitination, K27-linked ubiquitination, ERAD), indicating a cohesive module centered on tagging proteins for destruction and turnover. Some repair and stress signals (e.g., DNA damage checkpoint signaling) are present but appear linked through ubiquitin signaling rather than defining a separate function. Overall, the cluster represents components involved in ubiquitin-mediated protein turnover. ","confidence":"High","size":17,"edges":122,"triangles":525,"max_degree":16,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0051865","count":17},{"id":"GO:0030433","count":17},{"id":"GO:0070911","count":17},{"id":"GO:0051965","count":10},{"id":"GO:0031146","count":10}]},{"hash":"102458578543283267","title":"Ubiquitin-Dependent Immune Signaling","description":"The cluster is driven by GO terms tied to ubiquitination and protein degradation (ubiquitin-dependent proteolysis, protein ubiquitination, autoubiquitination, ERAD, K33-linked ubiquitination) and by immune signaling pathways (NF-kappaB regulation, JNK cascade, NOD2 signaling, B cell receptor signaling, memory T cell differentiation). Together these point to a theme of ubiquitin-mediated control of immune signaling and protein turnover.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0032088","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0046328","count":3}]},{"hash":"1152800746160080375","title":"Ubiquitin-Mediated Apoptosis and Immune Signaling","description":"The cluster centers on ubiquitination processes (polyubiquitination, ubiquitin-dependent proteolysis, ERAD) that regulate cell fate decisions such as apoptosis and necroptosis, while also modulating innate immune pathways (TLR signaling, NF-\u03baB via I\u03baB phosphorylation). This coherent pattern suggests proteins coordinating ubiquitin-driven control of cell survival and immune signaling.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"autophagy","top_go_terms":[{"id":"GO:0000209","count":6},{"id":"GO:0043066","count":4},{"id":"GO:0034121","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0030433","count":4}]},{"hash":"2193923503663703050","title":"Gene Expression Regulation and Stress-Activated Signaling","description":"The cluster centers on core gene expression control and RNA processing: DNA-templated transcription, DNA replication, pre-miRNA processing, miRNA-mediated silencing, and mRNA decay. The presence of Hippo signaling and intrinsic apoptotic pathways in response to ER and osmotic stress indicates coupling of these gene expression processes to stress-response signaling. This combination suggests a coherent theme of transcriptional and post-transcriptional regulation linked to cellular stress responses.","confidence":"High","size":17,"edges":87,"triangles":250,"max_degree":16,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":6},{"id":"GO:0070059","count":4},{"id":"GO:0035329","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0035278","count":3}]},{"hash":"2056807773819284175","title":"Steroid and Retinoid Lipid Metabolism with Prostaglandin Signaling","description":"The cluster is enriched for retinoid metabolism (retinol, retinal), steroid hormone biosynthesis (C21-steroid, androgen), bile acid biosynthesis, and a cellular response to prostaglandin D stimulus, plus related signaling cascades. This pattern points to a cohesive lipid- and hormone-metabolism module with active prostaglandin signaling influencing tissue homeostasis and stress responses, rather than a single isolated pathway.","confidence":"Medium","size":17,"edges":122,"triangles":561,"max_degree":16,"top_function":null,"top_go_terms":[{"id":"GO:0042574","count":14},{"id":"GO:0042572","count":14},{"id":"GO:0071799","count":10},{"id":"GO:0001894","count":10},{"id":"GO:0006699","count":10}]},{"hash":"1837822636301218194","title":"Nuclear transcription and RNA processing regulators","description":"The dominant GO terms point to nuclear activities: transcription regulation by RNA Pol II, regulation of transcription start site selection, and ncRNA-mediated gene silencing, along with several RNA processing steps (spliceosome-mediated splicing, snoRNA release from pre-rRNA, and rRNA turnover). There is also a hint of developmental involvement (embryonic cranial skeleton morphogenesis) and an outlier indicating DNA replication. Taken together, these proteins likely function in controlling gene expression at the transcriptional and RNA-processing levels in the nucleus, with potential ties to development. ","confidence":"Medium","size":17,"edges":6,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0045944","count":4},{"id":"GO:0031047","count":4},{"id":"GO:0048026","count":4},{"id":"GO:0048701","count":4}]},{"hash":"1280218701491258643","title":"Fungal mating and cell wall biosynthesis","description":"This cluster shows strong fungal-specific processes: karyogamy during mating and beta-glucan biosynthesis for the fungal cell wall, suggesting a function in fungal reproduction and wall assembly. Additional terms on protein folding stress (unfolded protein response, ER stress) and core cellular processes (DNA replication, iron-sulfur cluster assembly) indicate concurrent growth and stress-regulation activities. Overall, the dominant theme is fungal mating-related cell wall biosynthesis with supportive stress-response signals.","confidence":"Medium","size":17,"edges":18,"triangles":8,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:0070389","count":2},{"id":"GO:0016226","count":2},{"id":"GO:0070880","count":2},{"id":"GO:1903382","count":2}]},{"hash":"2008440413039023891","title":"Cardiovascular and neural development","description":"The top GO terms center on organogenesis-related processes: heart development, angiogenesis, and CNS development, with additional signals for cell proliferation and regulatory protein modifications (ubiquitination and homooligomerization). This suggests a coordinated developmental program affecting heart, vascular, and neural tissues, rather than a single isolated function.","confidence":"Medium","size":17,"edges":25,"triangles":19,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":5},{"id":"GO:0016567","count":5},{"id":"GO:0007507","count":4},{"id":"GO:0008284","count":4},{"id":"GO:0001525","count":4}]},{"hash":"156726220244617907","title":"Oxidative stress response and transcription regulation","description":"The cluster is enriched for oxidative stress and redox homeostasis terms (cell redox homeostasis; cellular response to oxidative stress; ER stress) alongside transcriptional regulation terms (positive regulation of DNA binding; negative regulation of transcription by RNA Pol II), suggesting a cohesive module where redox signaling interfaces with transcription control.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":7},{"id":"GO:0034976","count":6},{"id":"GO:0045454","count":6},{"id":"GO:0021762","count":5},{"id":"GO:1903206","count":5}]},{"hash":"2207210243889551614","title":"Steroid hormone biosynthesis and metabolism","description":"The cluster shows strong enrichment for steroid-related processes, including C21-steroid hormone biosynthetic process, androgen metabolism, progesterone metabolism, and bile acid biosynthesis, suggesting a common theme of hormone production and lipid metabolism. A few terms (naphthalene catabolic process, pyridoxal biosynthetic process) are less directly related but do not obscure the dominant steroid/hormone signal.","confidence":"Medium","size":17,"edges":95,"triangles":310,"max_degree":14,"top_function":null,"top_go_terms":[{"id":"GO:0071799","count":13},{"id":"GO:0001894","count":13},{"id":"GO:0006699","count":13},{"id":"GO:0018931","count":13},{"id":"GO:1901653","count":13}]},{"hash":"371350171067946338","title":"Cell cycle control and growth signaling","description":"The top GO terms cluster around regulation of the cell cycle (mitotic cycle, centrosome cycle, DNA replication regulation) and apoptosis, with several growth-related signaling pathways (Wnt, Hippo) also represented, indicating a theme of coordinating cell proliferation with growth and fate decisions.","confidence":"Medium","size":17,"edges":4,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006915","count":7},{"id":"GO:0045944","count":6},{"id":"GO:0007121","count":5},{"id":"GO:0000278","count":5},{"id":"GO:0010571","count":5}]},{"hash":"1637909050644947221","title":"Cellular Stress Response and Transport","description":"The top GO terms center on stress-related processes (SOS response and nucleotide-excision repair) and a broad set of transport/export activities (xenobiotic export, teichoic acid and bacteriocin transport, oligopeptide export, ceramide translocation, taurine transport), suggesting a functionally cohesive theme around stress-induced defense and material movement across membranes, even though the specific terms span diverse organisms. This points to a general cluster of stress response linked to transport. ","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009432","count":8},{"id":"GO:0046618","count":6},{"id":"GO:0006289","count":6},{"id":"GO:0015910","count":6},{"id":"GO:0015777","count":6}]},{"hash":"860940730769454784","title":"Cell-cycle, apoptosis, and innate immune signaling regulation","description":"This cluster's GO terms emphasize regulation of the cell cycle, negative regulation of apoptotic processes, transcriptional repression, and protein ubiquitination, with additional hints of innate immune pathway regulation (TLR signaling). There are also related terms for SRP-dependent targeting of proteins to membranes and nuclear ribosomal export, suggesting a broader role in coordinating protein synthesis and trafficking under stress. Taken together, the group appears to be a module of regulators controlling cell fate and immune signaling, through post-translational and transcriptional mechanisms.","confidence":"Medium","size":17,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":2},{"id":"GO:0034121","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0043066","count":2},{"id":"GO:0000209","count":2}]},{"hash":"2268500244635198255","title":"Genome stability and cell fate regulation","description":"These proteins co-occur with GO terms for DNA repair (mismatch repair), telomere maintenance (telomerase holoenzyme assembly), and cell cycle control, along with negative regulation of transcription, apoptosis, and ubiquitination. The common thread is genome stability maintenance and regulation of cell fate, with ancillary stress signaling. ","confidence":"Medium","size":17,"edges":26,"triangles":11,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0006457","count":2},{"id":"GO:0006298","count":2},{"id":"GO:1905323","count":2},{"id":"GO:0071157","count":1},{"id":"GO:0034121","count":1}]},{"hash":"1717803594982715483","title":"Transcription Regulation and Cardiac Development","description":"The cluster shows enrichment for transcription-related processes (RNA polymerase II and III activity, preinitiation complex assembly, and rRNA transcription) alongside heart- and muscle-development terms (adult heart development, third and fourth ventricle development, skeletal muscle cell differentiation). This suggests proteins grouped here may participate in transcription control with links to cardiac/muscle development pathways, even though there are no inferred interactions within the cluster.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0044030","count":2},{"id":"GO:0007512","count":2},{"id":"GO:0021592","count":2},{"id":"GO:0021678","count":2}]},{"hash":"1103398685970554059","title":"Protein Quality Control and Trafficking","description":"The GO terms center on intracellular protein handling: ribophagy, ER-to-cytosol and ER-to-Golgi transport, endosome-to-lysosome/MVB sorting, and quality-control pathways (ubiquitin-proteasome and nuclear QC), indicating a cohesive theme of protein turnover and trafficking within the cell.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034517","count":1},{"id":"GO:0030970","count":1},{"id":"GO:0051228","count":1},{"id":"GO:0034214","count":1},{"id":"GO:0032510","count":1}]},{"hash":"316925882600186370","title":"Ubiquitin-Dependent Protein Degradation & Cell Cycle","description":"This cluster is driven by ubiquitin-proteasome\u2013related processes: ubiquitin-dependent protein catabolic process, SCF-dependent and K11-linked ubiquitination, and ERAD-associated degradation, indicating a shared function in targeted proteolysis. The presence of metaphase/anaphase transition and cell division terms suggests coupling to cell-cycle regulation via degradation of key mitotic regulators. A few immune signaling terms (NLRP3 inflammasome assembly, TLR9 signaling) and negative regulation of apoptosis hint at broader roles for ubiquitin-modulated pathways in controlling cell fate. Overall, the theme is proteolysis and cell-cycle control linked by ubiquitination.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0007091","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0070979","count":2},{"id":"GO:0043066","count":2}]},{"hash":"1128044219190687079","title":"Endosomal-Vacuolar Protein Trafficking","description":"The terms cluster around transport between endosomes, Golgi, and vacuoles/lysosome, including late endosome to vacuole via multivesicular body sorting, early endosome to Golgi transport, and Golgi to endosome transport, plus endocytosis and vacuolar protein targeting. This suggests a cohesive theme of intracellular trafficking through endosomal compartments toward the vacuole/lysosome, with possible context of insect fat body storage protein routing. Confidence: High.","confidence":"","size":17,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0032511","count":1},{"id":"GO:0007565","count":1},{"id":"GO:0006623","count":1},{"id":"GO:0009997","count":1},{"id":"GO:0034498","count":1}]},{"hash":"1669951488687723087","title":"Unknown","description":"The top terms are spread across disparate processes (cardiac signaling, brown fat differentiation, cell migration, CD40 signaling, NF-kappaB regulation, ubiquitination, inflammatory cytokine production, ER stress\u2013related apoptosis, and membrane localization), with only one hit each and no clear shared pathway. The absence of edges or triangles suggests there is no cohesive functional module to name beyond Unknown.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086070","count":1},{"id":"GO:1903444","count":1},{"id":"GO:0016477","count":1},{"id":"GO:0023035","count":1},{"id":"GO:0007253","count":1}]},{"hash":"1919711738467199374","title":"Epigenetic Regulation of Transcription","description":"The cluster is dominated by GO terms for DNA-templated transcription and epigenetic processes, including DNA methylation and histone modification, suggesting a core theme of transcriptional control via chromatin state; a few terms are obsolete or broad, but the overall signal points to epigenetic regulation of gene expression.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0016310","count":1},{"id":"GO:0042594","count":1},{"id":"GO:0015970","count":1},{"id":"GO:0090116","count":1}]},{"hash":"1517502085894445336","title":"Mitochondrial Transport and Energy Regulation","description":"The cluster is dominated by GO terms tied to mitochondrial membrane regulation (permeability, potential) and transport (ADP, ATP, alpha-ketoglutarate, Mg2+), plus metabolic signaling responses to insulin/IGF stimuli. This pattern points to a cohesive function: control of mitochondrial energetics and substrate exchange, linking energy production to cellular signaling. Confidence in this connection is high.","confidence":"High","size":17,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0046902","count":10},{"id":"GO:0051881","count":10},{"id":"GO:0015742","count":10},{"id":"GO:0032869","count":10},{"id":"GO:1990314","count":10}]},{"hash":"1485587026635371481","title":"Unknown","description":"The GO terms cover several unrelated areas: Wnt signaling and oligodendrocyte differentiation (development), nematode molting and pharyngeal pumping (nematode biology), isotype switching and humoral immune response (immunology), and DNA replication/repair. With no edges or cohesive pathway linking the proteins, there is no clear common function binding the cluster. ","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":2},{"id":"GO:0048709","count":2},{"id":"GO:0018996","count":1},{"id":"GO:0043050","count":1},{"id":"GO:0045876","count":1}]},{"hash":"1335542631135313379","title":"Tissue development and differentiation","description":"The top GO terms cluster around developmental processes across multiple tissues\u2014lung mesenchyme, thymus, keratinocytes, and myotubes\u2014plus multicellular organism development and T cell differentiation. The presence of cell migration also supports morphogenesis. The collection thus represents proteins involved in tissue formation and lineage specification, hence this label.","confidence":"High","size":17,"edges":40,"triangles":32,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0060484","count":2},{"id":"GO:0034198","count":2},{"id":"GO:0030216","count":2},{"id":"GO:0032435","count":2}]},{"hash":"428531772593945423","title":"Bacterial cell wall biosynthesis and glycosylation","description":"The terms cluster around production of cell wall components and related glycan modifications: cell wall organization, teichoic acid and cellulose biosynthesis, UDP-glucose metabolism feeding glycosylation pathways, and O-linked protein glycosylation. This set points to biosynthesis of cell wall polysaccharides and glycoproteins in bacteria, rather than other cellular processes, making this label specific and representative.","confidence":"High","size":17,"edges":9,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0036108","count":2},{"id":"GO:0030213","count":2},{"id":"GO:0030244","count":2},{"id":"GO:0006011","count":2}]},{"hash":"1576920806437243522","title":"Unknown","description":"The GO terms are scattered across tissue-specific functions (renal water transport, corneocyte development) and broad regulatory processes (cell cycle, DNA recombination, PI signaling, xenobiotic response, glycogen synthase regulation). There is no single cohesive function linking them, so the cluster cannot be reliably named after a common theme.","confidence":"","size":17,"edges":5,"triangles":0,"max_degree":2,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:2001153","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0080111","count":3},{"id":"GO:1900087","count":3},{"id":"GO:0003335","count":3}]},{"hash":"1152093208211319520","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by translation and ribosome biogenesis terms, pointing to protein synthesis machinery and growth-related processes. Supporting signals in cell cycle and GTPase regulation further align with cellular growth and ribosome assembly dynamics. Additional metabolism terms (cholesterol biosynthesis, glutamine metabolism) likely reflect the broader metabolic state that accompanies ribosome production. Overall, the theme centers on building and supporting the protein synthesis apparatus during growth.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":2},{"id":"GO:0046939","count":2},{"id":"GO:0046940","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006412","count":2}]},{"hash":"2210334618597610982","title":"Unknown","description":"The GO terms span diverse biosynthetic and metabolic processes (antibiotic, PHB, melanin, mycolic acid, glucocorticoid, androgen, acetoin) plus a transcription regulation term and an obsolete oxidation-reduction term, with no clear unifying function. No interactions are reported (Edges 0), so there isn't a cohesive theme to name this cluster beyond Unknown.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":7},{"id":"GO:0042619","count":6},{"id":"GO:0055114","count":6},{"id":"GO:0006355","count":5},{"id":"GO:0006710","count":5}]},{"hash":"468995233463436771","title":"Unknown","description":"Unknown","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042823","count":2},{"id":"GO:0070455","count":2},{"id":"GO:1901006","count":2},{"id":"GO:1902128","count":2}]},{"hash":"2064577932366333823","title":"Ion transport and calcium signaling in muscle and neurons","description":"The cluster\u2019s top GO terms emphasize ion transport (calcium, potassium, manganese, phosphate) and related signaling in muscle contraction and neuronal communication (calcium import, skeletal muscle regulation, long-term potentiation, heart contraction, mitochondrial calcium homeostasis), suggesting a cohesive theme around ion homeostasis guiding muscle and neural signaling.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006817","count":1},{"id":"GO:0048022","count":1},{"id":"GO:0098735","count":1},{"id":"GO:0010163","count":1},{"id":"GO:0060291","count":1}]},{"hash":"1427872680379682201","title":"Ribosome biogenesis and translation","description":"The top GO terms are dominated by ribosome-related processes: ribosome biogenesis, ribosomal subunit export from nucleus, ribosomal small subunit biogenesis, and cytoplasmic translation, along with tRNA modification. This pattern points to a cohesive cluster centered on ribosome assembly and function, i.e., production of ribosomes and protein synthesis. A few terms about salt stress and cell cycle appear but do not override the primary ribosome-focused signal.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0006400","count":3},{"id":"GO:0000055","count":3},{"id":"GO:1901001","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1028324283297864030","title":"Nuclear dynamics and genome maintenance","description":"The top GO terms cluster around nuclear envelope remodeling during mitosis (disassembly/reassembly), meiotic chromatin organization in oocytes (karyosome formation), and genome-related processes such as DNA integration and regulation of viral genomes, plus DNA repair regulation. A few metabolic terms are present but the core theme is nucleus-centric genome organization and stability.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015074","count":1},{"id":"GO:0007084","count":1},{"id":"GO:0030717","count":1},{"id":"GO:0075713","count":1},{"id":"GO:0045071","count":1}]},{"hash":"134988286138012685","title":"Ribosome Biogenesis and Translation","description":"This cluster is dominated by GO terms related to ribosome assembly and function: ribosome biogenesis, cytoplasmic translation, tRNA modification, and export of the large ribosomal subunit from the nucleus, plus RNA editing that can affect translation fidelity. Together these suggest a coherent theme around ribosome assembly and protein synthesis.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006382","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0042254","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0000055","count":2}]},{"hash":"2152174343285331825","title":"Neural development and cytoskeletal remodeling","description":"The top GO terms point to brain/forebrain development and skeletal morphogenesis, suggesting involvement in CNS and craniofacial development. The Arp2/3 actin nucleation term indicates cytoskeletal remodeling essential for neuronal migration and morphogenesis, while ubiquitin-proteasome\u2013related processes imply regulated protein turnover during development. Together, these signals converge on neural development with cytoskeletal dynamics and proteostasis as core features.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0048705","count":1},{"id":"GO:0031146","count":1},{"id":"GO:0070317","count":1},{"id":"GO:0030900","count":1}]},{"hash":"797989208660414431","title":"Mitochondrial energy metabolism and transport","description":"Top GO terms center on mitochondrial membrane regulation, ATP/ADP and metabolite transport, and responses to metabolic signals and oxidative stress, indicating a coherent mitochondria-focused energy and metabolite-handling module.","confidence":"High","size":17,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070542","count":8},{"id":"GO:0046902","count":6},{"id":"GO:0051881","count":6},{"id":"GO:0015742","count":6},{"id":"GO:0032869","count":6}]},{"hash":"425397390238978946","title":"Diverse signaling and stress-response pathways","description":"GO terms cluster around multiple signaling cascades (positive regulation of protein serine/threonine kinase activity; SREBP signaling; smoothened signaling involved in dorsal/ventral neural patterning) and tissue development (retina development). Additional terms point to genome maintenance (telomere maintenance via telomerase; homologous recombination repair) and stress responses (cellular response to xenobiotic stimulus; hypoxia) as well as mRNA transport. The collection does not converge on a single function, but rather suggests a mix of signaling actions and cellular stress/genome maintenance roles, so the label reflects that broad, integrative theme.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071902","count":3},{"id":"GO:0032933","count":2},{"id":"GO:0060831","count":2},{"id":"GO:0060041","count":2},{"id":"GO:0007004","count":2}]},{"hash":"2063161960280023082","title":"Unknown","description":"The top GO terms are a patchwork: signals about smooth muscle cell proliferation regulation and PDGFR signaling exist, but there are also terms about osmotic stress, transcription via SRF, and DNA repair; several terms are obsolete. No single unifying function or pathway emerges for all 17 proteins, and the lack of edges suggests the proteins cover diverse roles. Therefore a generic Unknown label best reflects the cluster.","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010735","count":2},{"id":"GO:1904706","count":2},{"id":"GO:2000587","count":1},{"id":"GO:0071475","count":1},{"id":"GO:0001560","count":1}]},{"hash":"1380050724774364572","title":"Cardiovascular development and signaling","description":"This cluster is dominated by terms for heart development, cardiac muscle contraction, and blood vessel morphogenesis, suggesting a cardiovascular development/signal theme. Growth factor signaling (EGF, GM-CSF) appears among the terms, indicating broader signaling roles, though the core pattern points to cardiovascular biology.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0060048","count":2},{"id":"GO:0007205","count":2},{"id":"GO:0071364","count":2},{"id":"GO:0001782","count":2}]},{"hash":"821331379782821141","title":"Growth and differentiation regulation","description":"This cluster centers on cell growth (GO:0016049) and positive regulation of monocyte differentiation (GO:0045657), suggesting a theme of growth and lineage differentiation control. Other terms indicate related regulatory and stress-response activities (telomere maintenance, glucocorticoid response, lysosomal catabolic regulation, skin morphogenesis). The connections are diverse rather than tightly linked to a single pathway, so the label aims to reflect a broad growth/differentiation regulatory theme rather than a precise function.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016049","count":2},{"id":"GO:0045657","count":2},{"id":"GO:0000723","count":2},{"id":"GO:1904925","count":1},{"id":"GO:1903061","count":1}]},{"hash":"2118898871435013739","title":"Unknown","description":"The Top Terms span widely divergent processes (ubiquitination; RISC complex assembly; mRNA splicing; phosphorylation; polysaccharide metabolism such as alginic acid biosynthesis and pectin catabolism; developmental and cell cycle related terms), and there are no edges connecting the proteins. This indicates no coherent shared function or mechanism to label, so Unknown with no clear confidence. ","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0007253","count":2},{"id":"GO:0070923","count":1},{"id":"GO:0042121","count":1},{"id":"GO:0045490","count":1}]},{"hash":"982145121881151554","title":"Unknown","description":"The GO terms span neurodevelopment (forebrain development, neural tube closure), immune defense, and broad cellular processes (translation initiation, transcription, cell cycle, apoptosis) as well as stress responses (cadmium ion response, ER stress\u2013induced apoptosis). There is no single cohesive function that links these terms, suggesting the cluster may reflect diverse roles or a general regulatory set rather than a specific, well-defined module.","confidence":"","size":17,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030900","count":2},{"id":"GO:0001843","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0001731","count":2},{"id":"GO:0071276","count":2}]},{"hash":"274735610210405104","title":"Hypoxia-driven inflammation and calcium signaling","description":"Top GO terms cluster around hypoxia response and acute-phase/inflammatory response, plus cellular responses to xenobiotic stimuli and calcium signaling (including calcium release regulation and a calcium-modulating Wnt pathway). This pattern suggests a module tied to stress/inflammatory signaling with calcium dynamics. A couple of terms (embryo implantation, enterobacterial antigen biosynthesis) are less clearly connected and may reflect broader multifunctionality or annotation noise.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008284","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0007566","count":2},{"id":"GO:0006953","count":2},{"id":"GO:0035690","count":2}]},{"hash":"625299152843122661","title":"Developmental Transcription and Growth Regulation","description":"This cluster is dominated by GO terms for transcriptional regulation by RNA polymerase II (both negative and positive), along with multiple developmental and growth-related terms (midbrain development, pancreas morphogenesis, multicellular organism growth, smooth muscle cell migration). Elastin catabolic process points to tissue remodeling, and cytokine production terms suggest transcriptional control of inflammatory signals. Together, these terms imply proteins that coordinate gene expression during development and structural remodeling, with some involvement in inflammation.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":4},{"id":"GO:0030901","count":3},{"id":"GO:0045415","count":2},{"id":"GO:0050720","count":2},{"id":"GO:0060309","count":2}]},{"hash":"1963837481808130721","title":"RNA Modification and Biosynthesis","description":"This cluster shows enrichment for RNA modification terms (tRNA methylation, rRNA modification, mRNA capping) alongside multiple biosynthetic processes (antibiotic, biotin, polyamine, vitamin E). The combination suggests a group of proteins involved in both producing small molecules and modifying RNA, reflecting enzymes with roles in metabolism and RNA-processing machinery.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0009102","count":5},{"id":"GO:0006596","count":5},{"id":"GO:0016049","count":5},{"id":"GO:0030488","count":5}]},{"hash":"785810190214318536","title":"Glandular epithelial branching morphogenesis and adhesion","description":"This cluster centers on gland morphogenesis and epithelial proliferation (mammary and salivary glands), with strong signals for cell adhesion and responses to hepatocyte growth factor, pointing to a cohesive theme of branching morphogenesis and epithelial adhesion in glandular development. While there are related terms for signaling and apoptosis, the core pattern aligns with glandular epithelial morphogenesis and adhesion.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033601","count":2},{"id":"GO:0007155","count":2},{"id":"GO:0060665","count":1},{"id":"GO:0032733","count":1},{"id":"GO:0035729","count":1}]},{"hash":"82764149409121839","title":"Unknown","description":"The Top Terms are highly heterogeneous: plant-type secondary cell wall biogenesis, antibiotic biosynthesis, proteolysis, cocaine catabolic process, several signaling pathways (FGF receptor, GDNF receptor), lipoteichoic acid biosynthesis, colon epithelial cell migration, prostatic bud formation regulation, and choline biosynthesis. With no network connectivity (Edges 0, Triangles 0), there isn\u2019t a single cohesive function linking these proteins. Therefore, no meaningful unifying label can be assigned. ","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009834","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0006508","count":2},{"id":"GO:0050784","count":2},{"id":"GO:0040037","count":2}]},{"hash":"305473701970082784","title":"RNA metabolism and ribosome biogenesis","description":"This cluster prominently features RNA processing and ribosome-related functions: mRNA splicing via spliceosome, transcription termination/antitermination, rRNA pseudouridine synthesis, ribosome biogenesis, and maintaining translational fidelity. Together these terms suggest a module centered on RNA metabolism and the assembly and fidelity of the ribosome, with some peripheral terms like lipid metabolism or heat response being less central. Confidence: Medium","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031564","count":2},{"id":"GO:0045292","count":2},{"id":"GO:0006629","count":1},{"id":"GO:0042254","count":1},{"id":"GO:0045903","count":1}]},{"hash":"1515119950869633611","title":"Cardiac and skeletal muscle development","description":"The strongest terms are heart development, atrial septum morphogenesis, and skeletal muscle cell differentiation, pointing to differentiation programs for cardiac and skeletal muscle tissues. Additional terms like EGFR signaling and transcription regulation fit into broad developmental regulation, though there are outliers (e.g., IgA isotype switching). Overall, the cluster appears to reflect muscle/heart development with common regulatory processes.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007507","count":2},{"id":"GO:0048298","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0010452","count":2},{"id":"GO:0035914","count":2}]},{"hash":"1052406476731965115","title":"Innate Immune Sensing and Antigen Presentation","description":"The terms cluster around inflammasome assembly (NLRP3), TLR9 signaling, interferon-beta production, and antigen processing/presentation (MHC I, dendritic cells), plus xenophagy, indicating a cohesive theme of innate immune sensing leading to antigen handling and inflammatory signaling.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0044546","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0034162","count":2},{"id":"GO:0045359","count":2},{"id":"GO:0046827","count":2}]},{"hash":"162001483024383793","title":"Innate Immune Signaling Regulators","description":"Many of the top GO terms describe negative regulation of key immune signaling pathways (NF-kappaB activity, TLR signaling, and NOD2 signaling) and modulation of cell death (apoptosis and necroptosis). In addition, post-translational modifiers like poly-ADP-ribosylation and polyubiquitination suggest these proteins regulate signaling cascades rather than performing a single enzymatic function. Together, the terms point to a cluster of proteins that fine-tune innate immune responses and cell fate decisions; one outlier term about SA node communication is likely a misannotation or unrelated.","confidence":"Medium","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":3},{"id":"GO:0070212","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0071157","count":3},{"id":"GO:0034121","count":3}]},{"hash":"309085744413334468","title":"Unknown","description":"The top terms cover diverse processes (liver regeneration, lymphocyte and erythrocyte-related development, spleen/endothelium formation) and metal ion transport, with no clear, singular functional theme or interaction connecting them. The lack of edges also suggests heterogeneous roles, so a definite cluster label cannot be assigned. ","confidence":"","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097421","count":2},{"id":"GO:0060546","count":2},{"id":"GO:0019301","count":1},{"id":"GO:1903988","count":1},{"id":"GO:0043362","count":1}]},{"hash":"539478996219218214","title":"Nuclear transport and genome organization","description":"The cluster includes GO terms for DNA-templated transcription, mRNA and tRNA export from the nucleus, nuclear pore complex assembly/localization, telomere tethering to the nuclear periphery, and chromatin silencing at telomeres, along with nuclear membrane dynamics, suggesting a set of proteins coordinating transcription with nuclear transport and genome architecture.","confidence":"High","size":17,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0031990","count":1},{"id":"GO:0034398","count":1},{"id":"GO:0035392","count":1},{"id":"GO:0007184","count":1}]},{"hash":"885779116060753835","title":"Ubiquitination and Proteostasis","description":"This cluster is dominated by GO terms related to ubiquitination (autoubiquitination, ubiquitin-dependent ERAD, ubiquitin-dependent SMAD catabolic process, and K63-linked ubiquitination) and protein quality control, including chaperone-mediated protein complex assembly. While there are additional stress-response terms, the strongest signals point to ubiquitin tagging and degradation pathways that maintain proteostasis. Confidence: High","confidence":"","size":16,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0030579","count":5},{"id":"GO:0090035","count":4},{"id":"GO:0070534","count":4}]},{"hash":"2020683332553707954","title":"Multiorgan Development and Transcriptional Regulation","description":"The cluster shows enrichment for development-related GO terms across multiple organs (brain regions, heart, gonad, digestive tract, spleen) plus a regulatory term for transcription by RNA polymerase II, suggesting proteins that coordinate multicellular development via transcriptional control rather than a single tissue-specific function.","confidence":"High","size":16,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":7},{"id":"GO:0030901","count":4},{"id":"GO:0021983","count":4},{"id":"GO:0048536","count":4},{"id":"GO:0007275","count":4}]},{"hash":"684208962910789344","title":"Ubiquitination-Driven Degradation and NF-kB Signaling","description":"The top GO terms are dominated by ubiquitin-related processes (ubiquitin-dependent proteolysis, various ubiquitin linkages, autoubiquitination, histone ubiquitination) and connections to signaling pathways such as NF-kB and TNF, indicating a cluster of proteins involved in ubiquitin-mediated proteolysis and ubiquitin-regulated signaling. This combination supports a cohesive theme around ubiquitination machinery and its role in signaling and degradation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0042787","count":9},{"id":"GO:1903265","count":8},{"id":"GO:0036205","count":7},{"id":"GO:0051865","count":7},{"id":"GO:0085020","count":7}]},{"hash":"1324967096860206692","title":"Calcium-Dependent Cell Adhesion in Ectoderm Development","description":"This cluster is dominated by GO terms for calcium-dependent cell-cell adhesion, ectoderm development, and cell migration, with supporting signals of Wnt pathway regulation and general cell division processes. Together these point to a cohesive theme of calcium-mediated adhesion driving morphogenesis in ectodermal tissues, with coordinated cell movement and signaling modulation; the other terms likely reflect broader cellular functions present in the protein set. ","confidence":"Medium","size":16,"edges":31,"triangles":30,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:1904798","count":8},{"id":"GO:0086019","count":8},{"id":"GO:0071255","count":8},{"id":"GO:0032471","count":8},{"id":"GO:0086073","count":8}]},{"hash":"1892817489588410331","title":"Male Reproductive Development and Steroid Signaling","description":"Based on the Top Terms, the cluster is enriched for male sex differentiation (GO:0046661), steroid hormone receptor complex assembly (GO:0006463), and prostate gland development (GO:0030850), pointing to a shared role in androgen-driven male reproductive biology. Some terms related to ciliary processes (non-motile cilium assembly, photoreceptor outer segment localization) and basic cellular processes (snoRNP assembly, cell division) appear in the list but are less consistent with the main theme, suggesting the proteins may have dual roles or annotation overlaps. Overall, the core signal aligns with male reproductive development and steroid signaling.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046661","count":4},{"id":"GO:0006463","count":4},{"id":"GO:0030850","count":4},{"id":"GO:1903646","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1030310610820703275","title":"Cell Cycle and Apoptosis Regulators","description":"The cluster is dominated by GO terms about regulating the cell cycle, transcription by RNA polymerase II, apoptosis and necroptosis, and ubiquitination, suggesting the proteins function chiefly as regulators of cell cycle progression and programmed cell death, rather than forming a direct physical module. Some signals also touch on immune signaling (TLR regulation), but overall the common theme is regulation of cell fate and division.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0043066","count":3},{"id":"GO:0034121","count":2},{"id":"GO:0000209","count":2}]},{"hash":"350959082250329248","title":"Protein acetylation processes","description":"The top GO terms are dominated by various acetylation-related activities (N-terminal acetylation, peptidyl-lysine N6-acetylation, histone acetylation, and N-terminal propionylation), suggesting the cluster centers on acetylation modifiers or substrates. While there are related metabolic terms (acetoin, putrescine, N-acetylglucosamine, ectoine biosynthesis) and an occasional plant regulatory term (leaf formation), the acetylation theme is strongest and most representative of the cluster\u2019s function. ","confidence":"High","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045150","count":5},{"id":"GO:0009447","count":4},{"id":"GO:0018003","count":4},{"id":"GO:2000025","count":4},{"id":"GO:0006044","count":4}]},{"hash":"1252814004562515936","title":"Ubiquitin-mediated regulation of innate signaling and apoptosis","description":"The GO terms show a focus on regulating TLR signaling, necroptosis, apoptosis, transcription, and ubiquitination, with recurring mentions of polyubiquitination and autoubiquitination and NF-kB-related regulation (I-kappaB phosphorylation). This points to a cluster of regulators that modulate innate immune signaling and cell fate through ubiquitin pathways and chromatin/transcription control. Despite no edges, the functional themes align around ubiquitin-dependent modulation of immune signaling and apoptosis.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":2},{"id":"GO:0034121","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0043066","count":2},{"id":"GO:0000209","count":2}]},{"hash":"53492039496375472","title":"Unknown","description":"The top GO terms span DNA replication, transcription regulation, kinase signaling, protein folding, xenobiotic response, tetrapyrrole chemistry, plant hormone signaling, and immune regulation, with no single shared function dominating. This diversity prevents a cohesive, specific label for the cluster.","confidence":"","size":16,"edges":25,"triangles":0,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006261","count":1},{"id":"GO:0071902","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0017006","count":1},{"id":"GO:0032092","count":1}]},{"hash":"325774287082932205","title":"Chromatin remodeling and histone modification","description":"This cluster\u2019s GO terms heavily point to epigenetic regulation, including chromatin remodeling, histone acetylation (N-terminal lysine acetylation, histone H3-K14 acetylation), and heterochromatin regulation, all of which tie to controlling transcription accessibility. While a few terms are development- or pathway-focused or obsolete, the core themes revolve around chromatin state and transcriptional regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035948","count":1},{"id":"GO:2000219","count":1},{"id":"GO:0018076","count":1},{"id":"GO:1903699","count":1},{"id":"GO:0044154","count":1}]},{"hash":"547552809358698050","title":"Heterochromatin Maintenance and Telomere Regulation","description":"These proteins cluster around chromatin silencing and heterochromatin maintenance, including nucleosome density/positioning, DNA methylation-dependent heterochromatin, heterochromatin maintenance, and telomere maintenance, with some outliers related to nucleolar rDNA localization. Overall signal points to a chromatin regulation/genome stability function.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0060303","count":2},{"id":"GO:0016584","count":2},{"id":"GO:0030466","count":1},{"id":"GO:0061734","count":1},{"id":"GO:0070845","count":1}]},{"hash":"2191754980999147060","title":"Plant telomere and chromatin regulation","description":"The prominent telomere-related terms (rDNA heterochromatin formation, negative regulation of establishment of RNA/protein localization to telomeres) together with a connection to chromatin state and genome maintenance (DSB repair via sister chromatid exchange) suggest a theme centered on telomere biology and chromatin regulation in plants. While other terms (hormone responses, viral processes) appear, they are less cohesive with the core telomere/chromatin signals.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009739","count":1},{"id":"GO:1900033","count":1},{"id":"GO:1990414","count":1},{"id":"GO:1905778","count":1},{"id":"GO:0016032","count":1}]},{"hash":"885443628660345736","title":"Ciliary and Flagellar Assembly and Motility","description":"The top GO terms are dominated by axoneme/cilium-related processes: sperm axoneme assembly, regulation and movement of cilia, and flagellated sperm motility, plus protein modifications (polyglycylation, polyglutamylation) on microtubules that support ciliary/flagellar structure. Microtubule severing and epithelial cilium movement further reinforce a cilium/flagellum-centric cluster. A couple of metabolic terms seem peripheral. Overall, the cluster centers on ciliary/flagellar formation and movement.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018094","count":1},{"id":"GO:0007288","count":1},{"id":"GO:0003353","count":1},{"id":"GO:0030516","count":1},{"id":"GO:1905419","count":1}]},{"hash":"267827348237047309","title":"Unknown","description":"Top terms show organelle RNA processing and mitochondrial translation/assembly alongside unrelated processes (vulval location, gastric acid secretion, brown fat differentiation, calcium channel transport), making a single cohesive function unlikely. Because there is no clear, unified theme linking all terms, Unknown is the appropriate label.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045739","count":1},{"id":"GO:0030261","count":1},{"id":"GO:1901259","count":1},{"id":"GO:0000963","count":1},{"id":"GO:0045333","count":1}]},{"hash":"2099956279232429719","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060075","count":1},{"id":"GO:0050976","count":1},{"id":"GO:0030007","count":1},{"id":"GO:0098914","count":1},{"id":"GO:0071805","count":1}]},{"hash":"117454089078753095","title":"Diverse small-molecule solute transporters","description":"This cluster\u2019s top GO terms all point to transmembrane transport of various small molecules (nitrate, nitrite, arabinose, glucose, urate, trehalose, dehydroascorbic acid, sodium ions, etc.). The low connectivity (one edge) suggests a collection of transporters with different substrates rather than a single, cohesive pathway, so naming them as a general group of solute transporters captures the shared function while acknowledging substrate diversity. The lone GO term about replicative senescence is likely incidental rather than indicative of the cluster\u2019s main role.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":1},{"id":"GO:1904728","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0044381","count":1},{"id":"GO:0015747","count":1}]},{"hash":"138871190576093707","title":"Stress-Responsive Apoptosis and Cell-Cycle Regulation","description":"These proteins co-occur with GO terms pointing to cellular stress responses (xenobiotic, hydrogen peroxide, peptide hormone stimulus) and apoptosis, along with modulation of the cell cycle (G1/S transition). While a few terms like renal water transport and lipid A biosynthesis are less coherent with this theme, the dominant signal is stress-induced signaling that can trigger apoptosis and influence cell-cycle progression.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0071375","count":3},{"id":"GO:0070301","count":3},{"id":"GO:0006915","count":3}]},{"hash":"39174114107960856","title":"Nucleocytoplasmic Transport and DNA Replication","description":"This cluster is dominated by nuclear-related processes: mRNA export, ribosomal protein import, and nuclear pore complex assembly, alongside core DNA replication and cell division activities (DNA replication, chromatid cohesion). While some terms touch on regulatory or stress responses, the strongest pattern ties to nuclear transport and replication/cell cycle functions, justifying a label that emphasizes these themes.","confidence":"Medium","size":16,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006406","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0006260","count":4},{"id":"GO:0034599","count":4},{"id":"GO:0051754","count":4}]},{"hash":"317441428299982018","title":"Biosynthetic Pathways and Lipid Metabolism","description":"Most of the top GO terms describe biosynthetic processes (antibiotic biosynthesis, nonribosomal peptide biosynthesis, globoside and mannosyl-inositol phosphorylceramide biosynthesis) and related endoplasmic reticulum organization, suggesting a common theme around biosynthesis and membrane-associated lipid production. A few terms touch on translation or catabolism, reflecting broader metabolic roles in this cluster. Overall, the cluster appears enriched for biosynthetic activity, with a lipid metabolism orientation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0043041","count":2},{"id":"GO:0001576","count":1},{"id":"GO:0036210","count":1},{"id":"GO:0051999","count":1}]},{"hash":"1950402224994107855","title":"Membrane Transport and ER-Golgi Trafficking","description":"This cluster centers on membrane transport processes: vesicle trafficking between ER and Golgi and various ion/organic substrate transports, with apoptosis term as a minor outlier.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000269","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0015699","count":1},{"id":"GO:0015700","count":1},{"id":"GO:0043251","count":1}]},{"hash":"596965881427552908","title":"Innate antiviral and interferon response","description":"The top GO terms are dominated by innate immunity and antiviral signaling: innate immune response, cellular response to dsRNA, response to type I interferon, and defense response to virus. While there are also terms related to cell division and hormone-related processes, the strongest and most recurrent signals center on antiviral/immune pathways, suggesting this cluster reflects innate antiviral responses with some secondary regulatory roles. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":4},{"id":"GO:0071357","count":4},{"id":"GO:0043278","count":3},{"id":"GO:0071360","count":3},{"id":"GO:0046661","count":3}]},{"hash":"1877106241458380135","title":"Rho/Rap Signaling Regulators and Exocytosis","description":"Overall, these terms cluster around regulatory roles in signaling pathways (Rho, Rap, PDGFR\u03b2), with supporting processes in vesicle transport (exocytosis) and aspects of cell division (mitotic spindle assembly). The common theme is modulators of signaling and trafficking that influence cell shape, movement, and division.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010735","count":2},{"id":"GO:0090307","count":2},{"id":"GO:1904706","count":2},{"id":"GO:0032508","count":2},{"id":"GO:0006887","count":2}]},{"hash":"26514741366814566","title":"Bacterial envelope biosynthesis and stress response","description":"The cluster is enriched for GO terms tied to cell envelope construction and maintenance, including lipid A biosynthesis and lipopolysaccharide biosynthetic processes, as well as spore wall assembly and biofilm formation. The presence of base-excision repair and cellular response to hydrogen peroxide suggests concurrent oxidative damage defense, a common facet of envelope stress response. While a couple terms are obsolete or peripheral, the dominant theme points to envelope biosynthesis and stress management.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":2},{"id":"GO:0070301","count":2},{"id":"GO:0006284","count":2},{"id":"GO:0009245","count":1},{"id":"GO:0042244","count":1}]},{"hash":"795733841098616147","title":"RNA Processing and Proteostasis","description":"The top GO terms cluster around RNA processing (spliceosomal snRNP assembly, regulatory ncRNA-mediated gene silencing) and proteostasis-related stress responses (response to unfolded protein, chaperone-mediated protein folding, ER-associated ubiquitin-dependent protein catabolic process). Although some terms are obsolete and one plant hormone-related term appears, the dominant pattern links RNA regulation with protein quality control, suggesting a module combining RNA processing with proteostasis.","confidence":"Medium","size":16,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0010372","count":1},{"id":"GO:0031047","count":1},{"id":"GO:0000387","count":1},{"id":"GO:0051348","count":1},{"id":"GO:0016576","count":1}]},{"hash":"2280386092092102118","title":"Antiviral innate immune response","description":"The cluster is dominated by GO terms related to responses to type I interferon, exogenous dsRNA, and innate immune defense against viruses, suggesting an antiviral innate signaling program. While a few terms reference cell division and hormone-related development, these are less central to the main theme. Overall, the pattern points to antiviral/IFN-mediated activity.","confidence":"Medium","size":16,"edges":28,"triangles":5,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0071357","count":7},{"id":"GO:0051301","count":7},{"id":"GO:0071360","count":6},{"id":"GO:0008277","count":6},{"id":"GO:0045087","count":6}]},{"hash":"2234317067053076460","title":"Chemokine-Driven Inflammatory Signaling","description":"The top GO terms point to chemokine production (MIP-1\u03b1, CCL5) and NF-\u03baB\u2013related inflammatory signaling, along with associated cell migration, which together reflect an inflammatory immune-response cluster. Additional terms about heart signaling, mechanosensation, and hepatocyte apoptosis are likely indirect or broader tissue-context items rather than core drivers, so the central theme is inflammation and chemokine-mediated communication. This leads to a concise, specific label that captures the core function without overreaching.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086070","count":2},{"id":"GO:1903444","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0007253","count":2},{"id":"GO:0072660","count":2}]},{"hash":"1904730918046548402","title":"Glomerular development and filtration","description":"The top GO terms are strongly centered on kidney biology, notably glomerular basement membrane development and glomerular filtration, which suggests a cluster theme around glomerulus/kidney development and associated extracellular matrix processes. While other terms (e.g., CNS development, chemotaxis, cartilage development) are present, the renal-related terms provide the most coherent, representative signal for naming. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030194","count":3},{"id":"GO:0031214","count":3},{"id":"GO:0032836","count":3},{"id":"GO:0003094","count":3},{"id":"GO:0060686","count":3}]},{"hash":"1086799033222161274","title":"Mitochondrial Transport and Energy Regulation","description":"This cluster is driven by GO terms related to mitochondrial membrane dynamics and transport of key energy-related metabolites (ADP, ATP, alpha-ketoglutarate, magnesium) across mitochondrial membranes, as well as regulation of membrane permeability and potential. The inclusion of insulin/IGF signaling responses and oxidative stress (superoxide) further supports a coordinated mitochondrial energy metabolism and signaling theme. Overall, the proteins appear to function in mitochondrial transport and bioenergetics.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070542","count":4},{"id":"GO:0046902","count":3},{"id":"GO:0051881","count":3},{"id":"GO:0015742","count":3},{"id":"GO:0032869","count":3}]},{"hash":"876650835056372820","title":"Calcium signaling in heart and brain development","description":"The GO terms cluster around heart development and blood vessel morphogenesis, neuronal synaptic plasticity, and calcium ion release regulation, pointing to a calcium-dependent signaling module active in both cardiovascular and neural contexts. While a few terms are related to metabolism or xenobiotic response and some entries are obsolete, the shared theme is calcium-driven signaling tied to development in heart and brain.","confidence":"Medium","size":16,"edges":7,"triangles":0,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000272","count":4},{"id":"GO:0097274","count":4},{"id":"GO:0001569","count":3},{"id":"GO:1901841","count":3},{"id":"GO:1900271","count":3}]},{"hash":"1663944502061024900","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070301","count":2},{"id":"GO:0033129","count":2},{"id":"GO:0070935","count":2},{"id":"GO:0006740","count":2},{"id":"GO:0015940","count":2}]},{"hash":"785610403320705459","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061158","count":6},{"id":"GO:1903883","count":6},{"id":"GO:0001519","count":6},{"id":"GO:0010586","count":6},{"id":"GO:0035278","count":6}]},{"hash":"1553178657187835111","title":"Unknown","description":"The GO terms span metabolism (beta-ketoadipate pathway, glucose metabolism, pentose phosphate shunt) and diverse immune and developmental processes (T cell activation, foam cell differentiation regulation, phagocytic engulfment, cholesterol response, platelet aggregation, cell adhesion, mesoderm differentiation), with no single dominant theme tying all proteins together. This suggests a heterogeneous set of functions rather than a cohesive cluster.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"extracellular matrix organization","top_go_terms":[{"id":"GO:0042952","count":4},{"id":"GO:0006006","count":4},{"id":"GO:0006098","count":4},{"id":"GO:0010745","count":4},{"id":"GO:0002291","count":4}]},{"hash":"142008618558782768","title":"Unknown","description":"Unknown","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007568","count":10},{"id":"GO:0043547","count":10},{"id":"GO:0007283","count":7},{"id":"GO:0043066","count":6},{"id":"GO:1902679","count":6}]},{"hash":"1223589619351030861","title":"Endocrine development and hormone signaling","description":"Among the top GO terms, thyroid hormone metabolic process and adenohypophysis morphogenesis point to endocrine development and regulatory signaling. The response to cAMP and gene expression terms further support transcriptional programs tied to hormonal signaling. Some terms may reflect broader stress or species-specific developmental processes, but the endocrine theme remains the strongest thread.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042403","count":3},{"id":"GO:1902177","count":2},{"id":"GO:0010467","count":2},{"id":"GO:0008365","count":2}]},{"hash":"1185571686074866053","title":"Plant Floral Development and Epigenetic Regulation","description":"The terms center on plant development (floral meristem growth, bract development, auxin-related patterning) and gene regulation (transcription, DNA methylation/imprinting), suggesting a module focused on plant developmental control through transcriptional and epigenetic mechanisms, despite some obsolete entries.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060774","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0010451","count":1},{"id":"GO:0010186","count":1},{"id":"GO:0044026","count":1}]},{"hash":"1496051801109208867","title":"Unknown","description":"The terms span metabolism (ubiquinone and lipid homeostasis), neural development (Purkinje cell morphogenesis), and innate immune signaling (defense responses, xenophagy, IFN-\u03b2, LPS). With no clear, single functional theme and no interactions linking them, there isn\u2019t a cohesive cluster function to label beyond Unknown.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901006","count":2},{"id":"GO:0010795","count":2},{"id":"GO:0055088","count":2},{"id":"GO:0021692","count":2},{"id":"GO:1902171","count":2}]},{"hash":"4991742518675121","title":"Brain epigenetic chromatin remodeling and fear behavior","description":"These proteins show enrichment for epigenetic regulation (chromatin remodeling, DNA methylation-dependent heterochromatin formation) and neural/behavioral terms (fear response, maternal behavior), suggesting a brain-associated module where chromatin state influences fear-related and maternal behaviors. The presence of several obsolete terms reduces precision, but the core non-obsolete terms point to a coherent epigenetic-neural theme.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035948","count":3},{"id":"GO:0043044","count":3},{"id":"GO:0006349","count":3},{"id":"GO:0051567","count":3},{"id":"GO:0090309","count":2}]},{"hash":"604655861572792513","title":"Cardiac inflammatory chemokine signaling","description":"The top GO terms point to intercellular signaling in the heart (SA node to atrial cardiac muscle cell communication) and regulation of inflammatory chemokines (e.g., MIP-1\u03b1/CCL3 and CCL5), suggesting a cluster of proteins involved in cardiac signaling linked to inflammatory mediator production. While some terms also touch on NF-kappaB regulation and mechanosensation, the strongest shared theme appears to be heart-related signaling coupled with inflammatory chemokine activity, with a few unrelated annotations that may reflect broad functional annotations. Overall, a concise label capturing cardiac signaling with inflammatory chemokine output fits best.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086070","count":4},{"id":"GO:1903444","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0007253","count":4},{"id":"GO:0072660","count":4}]},{"hash":"995202776396652428","title":"Prostate development and hormone signaling","description":"The top GO terms point to male reproductive development (prostate gland development, male sex differentiation) and hormonal signaling pathways (steroid hormone receptor complex assembly, transforming growth factor beta receptor signaling, SMAD-related assembly). While there are also general processes like cell cycle/division and cellular trafficking, the strongest signals cluster around hormone-driven development of male reproductive tissue. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0007183","count":2},{"id":"GO:0007179","count":2}]},{"hash":"1701056805678522029","title":"Nuclear RNA processing & RNP assembly","description":"The terms cluster around nuclear RNA maturation and ribonucleoprotein assembly: ribosome biogenesis, snoRNA/snRNA pseudouridine synthesis, box H/ACA snoRNP assembly, and telomerase RNA localization/stabilization and holoenzyme assembly. These together indicate a cohesive theme of RNA processing and RNP complex formation; a few outlier terms about ubiquinone biosynthesis and lipid homeostasis appear incidental. ","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:1904874","count":1},{"id":"GO:0090669","count":1},{"id":"GO:0000454","count":1},{"id":"GO:0031120","count":1}]},{"hash":"758197509416540540","title":"Unknown","description":"The top GO terms span disparate processes (nervous system development and innervation; glial signaling; various developmental and tissue-formation terms) and include unrelated bacterial biosynthetic activity, with no single coherent function tying all proteins together. This makes a concise, representative label impossible.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0040037","count":3},{"id":"GO:0035860","count":3},{"id":"GO:0070395","count":3},{"id":"GO:0061580","count":3},{"id":"GO:0060686","count":3}]},{"hash":"1334620282674072739","title":"Synaptic vesicle recycling and glutamatergic signaling","description":"Based on the top terms, the cluster centers on neuronal endocytosis/recycling (receptor recycling, regulation of endosome size) and synaptic transmission, particularly glutamatergic signaling, with supporting links to cytoskeletal dynamics via Rho signaling. Although several terms are obsolete, the remaining functional terms cohere around vesicle trafficking and neurotransmission in neurons.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0060316","count":5},{"id":"GO:0097274","count":3},{"id":"GO:0001881","count":3},{"id":"GO:0051036","count":3},{"id":"GO:0035023","count":3}]},{"hash":"347641586592706417","title":"Chromatin modifiers and transcription regulators","description":"The top GO terms point to chromatin-level regulation and transcription control, including histone methylation/demethylation (peptidyl-lysine dimethylation, H3-K36 methylation), protein deubiquitination, and both positive and negative regulation of RNA polymerase II\u2013driven transcription, plus links to the p53-mediated DNA damage response. Developmental terms for heart and skeletal muscle suggest roles in tissue-specific transcription programs. Overall, these proteins appear to cluster around chromatin state management and transcription regulation rather than a single pathway.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045184","count":2},{"id":"GO:0007507","count":2},{"id":"GO:0018027","count":2},{"id":"GO:0048642","count":2},{"id":"GO:1900037","count":2}]},{"hash":"536650615605297116","title":"Small-molecule biosynthesis","description":"This cluster\u2019s top GO terms are dominated by biosynthetic processes, including biotin, antibiotic, cobalamin, and sterol biosynthesis, pointing to a theme of metabolite production. Other terms like methylation and cellular growth are present but less central, so the strongest, most representative label is small-molecule biosynthesis. ","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0009102","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0043985","count":3},{"id":"GO:0016049","count":3}]},{"hash":"487921246598239933","title":"Mechanotransduction and ubiquitination","description":"Top GO terms are dominated by cellular response to mechanical stimulus and protein ubiquitination, which points to a functional theme around sensing mechanical cues and regulating protein turnover. Additional signals related to cell migration, membrane protein localization, and inflammatory signaling suggest the cluster captures broader stress-response and signaling processes that interface with mechanotransduction. Some entries are obsolete, reflecting past annotations.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":5},{"id":"GO:0071260","count":5},{"id":"GO:0086070","count":4},{"id":"GO:1903444","count":4},{"id":"GO:0016477","count":4}]},{"hash":"1366571577025520009","title":"Organelle RNA Processing (mitochondria, chloroplasts)","description":"Based on GO terms dominated by mitochondrial translation, mitochondrial mRNA processing, and chloroplast RNA processing, the proteins in this cluster appear connected by organellar RNA metabolism. While some terms reference development or signaling, the strongest recurring theme centers on RNA processing in mitochondria and chloroplasts, supporting this label as representative of the cluster\u2019s function.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070129","count":1},{"id":"GO:0090615","count":1},{"id":"GO:0031425","count":1},{"id":"GO:0071908","count":1},{"id":"GO:0008277","count":1}]},{"hash":"257062466643647526","title":"Cell growth, division, and cytoskeleton remodeling","description":"This cluster centers on processes tied to protein turnover (ubiquitin-proteasome degradation), ribosome biogenesis, cell cycle progression, and actin-dependent cytoskeleton dynamics, all of which support cellular growth and division. While most terms align with proliferation and structural remodeling, a couple (defense response to Gram-positive bacteria and skeletal system morphogenesis) are less central, suggesting some pleiotropy but the main theme remains growth/division-related.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0000747","count":3},{"id":"GO:0051260","count":3},{"id":"GO:0042254","count":3}]},{"hash":"515900095522551692","title":"Innate Antiviral Signaling and Cell Migration","description":"The top GO terms are dominated by innate immune and antiviral responses (innate immune response, cellular response to type I interferon, cellular response to dsRNA, and defense-virus aspects), with additional terms related to integrin activation and cell migration, suggesting a theme where antiviral signaling is linked to cell movement/adherence. Some terms (heart development, cell division) are less aligned, but the primary signal supports this immune-migration axis.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045087","count":2},{"id":"GO:0071357","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0050689","count":1},{"id":"GO:0071360","count":1}]},{"hash":"1280004228946237660","title":"Vitamin/cofactor and antibiotic biosynthesis with stress responses","description":"This cluster is enriched for biosynthetic processes of vitamins and cofactors (cobalamin, biotin, menaquinone), as well as glucosylglycerol, and includes antibiotic biosynthesis; together they define a core theme of small-molecule biosynthesis. The presence of GO terms related to cellular responses to heat and desiccation suggests these biosynthetic activities are linked to stress-related metabolite production or protection, giving a coherent interpretation of the cluster as biosynthesis-focused with stress-response context.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":4},{"id":"GO:0009102","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0070415","count":2},{"id":"GO:0034605","count":2}]},{"hash":"325977240533268660","title":"Unknown","description":"The top GO terms span gene expression regulation (transcription, miRNA silencing, mRNA transport) and processes linked to cell cycle, cytoskeleton dynamics, and stress responses, with no obvious unifying function. Without a coherent theme, a precise, descriptive label cannot be confidently assigned.","confidence":"","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0043547","count":4},{"id":"GO:0006351","count":3},{"id":"GO:0035278","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0030042","count":3}]},{"hash":"1460115874302893034","title":"TLR/NOD2 inflammasome signaling","description":"The top GO terms point to core innate immune pathways\u2014TLR signaling (regulation), NOD2 signaling, and NLRP3 inflammasome assembly\u2014with supporting processes like ubiquitination and necroptotic/apoptotic regulation, indicating a cohesive theme of innate immune sensing and inflammasome-driven inflammation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0032088","count":4},{"id":"GO:0070431","count":4},{"id":"GO:0000122","count":3},{"id":"GO:0043066","count":3},{"id":"GO:0034121","count":3}]},{"hash":"1910745128881292879","title":"Immune Response and Inflammatory Regulation","description":"This cluster is dominated by GO terms related to immune system processes, inflammatory response, cytokine production (including IL-12), and regulation of T cell apoptosis, suggesting proteins that coordinate inflammatory signaling and adaptive immune responses. The presence of kynurenic acid biosynthetic process aligns with immunometabolic regulation (kynurenine pathway). A term like swimming behavior appears less relevant, likely representing broad or incidental annotations. Overall, the cluster appears to reflect immune activation and inflammatory regulation.","confidence":"High","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032735","count":1},{"id":"GO:0002534","count":1},{"id":"GO:0034276","count":1},{"id":"GO:0002376","count":1},{"id":"GO:0002678","count":1}]},{"hash":"471719378971572221","title":"Chloroplast Thylakoid Organization and NPQ","description":"The top GO terms are dominated by plant chloroplast functions\u2014granum assembly, thylakoid membrane organization, nonphotochemical quenching, and response to karrikin\u2014pointing to photosynthesis regulation. Some unrelated terms appear as noise, suggesting cross-species annotations, but the core theme is chloroplast light-harvesting regulation.","confidence":"Medium","size":16,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0090391","count":1},{"id":"GO:0010027","count":1},{"id":"GO:0080167","count":1},{"id":"GO:0010196","count":1}]},{"hash":"1561510407949872799","title":"Unknown","description":"The top GO terms span neural and lung development (optic nerve morphogenesis, corpus callosum development, lung-associated mesenchyme) alongside immune signaling, metabolism regulation, and stress responses, with no single unifying function to define a cohesive label.","confidence":"","size":15,"edges":93,"triangles":328,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016477","count":15},{"id":"GO:0010898","count":15},{"id":"GO:0060484","count":15},{"id":"GO:0022038","count":15},{"id":"GO:0050853","count":15}]},{"hash":"2004553632348636436","title":"LDL receptor regulation and cholesterol transport","description":"The cluster\u2019s terms cluster around LDL receptor\u2013mediated uptake and cholesterol transport, including LDL receptor catabolic process, negative and positive regulation of LDL particle clearance, regulation of receptor\u2013mediated endocytosis in cholesterol transport, and receptor recycling. This points to a cohesive theme of lipoprotein trafficking and cholesterol homeostasis, with a few peripheral terms (e.g., zygotic axis determination) that are less central to this function. ","confidence":"Medium","size":15,"edges":14,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0007354","count":3},{"id":"GO:0032802","count":3},{"id":"GO:0010989","count":3},{"id":"GO:0002001","count":3},{"id":"GO:0032902","count":3}]},{"hash":"631252597166702830","title":"Heat-shock response and protein quality control","description":"The top terms cluster around response to heat, unfolded protein response, ER protein folding, and ubiquitin-proteasome\u2013mediated quality control, suggesting a proteostasis/heat-stress module. While there are some peripheral terms like DNA replication and a signaling pathway, the dominant theme is heat-related protein folding and quality-control processes.","confidence":"High","size":15,"edges":79,"triangles":226,"max_degree":13,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":7},{"id":"GO:0006260","count":7},{"id":"GO:1900035","count":7},{"id":"GO:1901621","count":7},{"id":"GO:0034975","count":7}]},{"hash":"2204774048578731161","title":"Glycoprotein glycosylation and epithelial polarity","description":"The top GO terms cluster around glycosylation processes (notably O-linked hydroxyproline glycosylation and arabinogalactan protein metabolism), mucilage biosynthesis, and the maintenance of epithelial polarity/adhesion (root hair development and egg chamber follicle cells). This points to a module centered on cell-surface glycoproteins (like AGPs) and their role in cell surface architecture, signaling, and adhesive/polarity roles across plant and insect epithelia, with accompanying surface structure formation.","confidence":"Medium","size":15,"edges":74,"triangles":167,"max_degree":13,"top_function":null,"top_go_terms":[{"id":"GO:0075015","count":3},{"id":"GO:0030311","count":3},{"id":"GO:0042248","count":3},{"id":"GO:0010405","count":3},{"id":"GO:0001744","count":3}]},{"hash":"271632535485035486","title":"Redox-regulated metabolism and insulin signaling","description":"The terms cluster around redox balance (cell redox homeostasis, glutathione metabolism, protein glutathionylation) and core metabolic pathways (glycolysis, fatty acid beta-oxidation) with insulin- and xenobiotic-related responses. This suggests a set of proteins that coordinate energy metabolism under redox control and influence insulin signaling/secretion.","confidence":"Medium","size":15,"edges":18,"triangles":5,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0006096","count":2},{"id":"GO:0006749","count":2},{"id":"GO:0010731","count":2},{"id":"GO:0014823","count":1}]},{"hash":"969783380822008839","title":"Cell cycle and DNA replication proteins","description":"The top GO terms are dominated by DNA replication, G1/S transition, centrosome cycle, and meiotic cell cycle, indicating a coherent theme around cell-cycle progression and genome duplication. Kinetochore localization further supports chromosome segregation aspects. The other terms (nerve development, drug response, immune defense) seem peripheral, likely due to multifunctional proteins or annotation noise, but do not override the central cell-cycle signal.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0042220","count":5},{"id":"GO:0000082","count":5},{"id":"GO:0060079","count":5},{"id":"GO:0034501","count":5}]},{"hash":"2281533524830400109","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009636","count":10},{"id":"GO:0007014","count":10},{"id":"GO:1903265","count":10},{"id":"GO:0061158","count":10},{"id":"GO:1903883","count":10}]},{"hash":"1389287233891568615","title":"DNA Replication and Repair Complexes","description":"The top GO terms are heavily skewed toward DNA replication and DNA damage response/repair, including DNA replication, mitotic DNA replication checkpoint signaling, UV-damage excision repair, and error-free translesion synthesis. Additionally, there is a strong signal for protein assembly/oligomerization (homooligomerization, hexamerization) and assembly-related processes, suggesting these proteins form or stabilize multi-subunit complexes involved in genome maintenance. Some peroxisomal/mitochondrial assembly terms appear, but the core signal points to replication and repair machinery with complex assembly.","confidence":"Medium","size":15,"edges":17,"triangles":4,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0016562","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0034214","count":3},{"id":"GO:0034551","count":3}]},{"hash":"1880966772060262820","title":"Membrane Transport and Detoxification","description":"The set of top GO terms is dominated by transport-related activities\u2014export/import of xenobiotics, antibiotics, oligopeptides, teichoic acids, bacteriocins, and lipids across membranes or organelles\u2014suggesting a cluster of transporter/detoxification proteins. A nucleotide-excision repair term is present but appears less connected to the main theme.","confidence":"Medium","size":15,"edges":24,"triangles":8,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":6},{"id":"GO:0046618","count":4},{"id":"GO:0006289","count":4},{"id":"GO:0015910","count":4},{"id":"GO:0015777","count":4}]},{"hash":"1877744676888033885","title":"Telomere maintenance and cell cycle regulation","description":"The cluster\u2019s top GO terms concentrate on telomere maintenance via telomerase, telomere capping, and regulation of cyclin-dependent kinase activity, pointing to a shared theme of genomic stability and cell-cycle control. While some terms touch on muscle stretch response and fat cell differentiation, these appear peripheral to the dominant telomere and cell cycle signals.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":2},{"id":"GO:0007049","count":2},{"id":"GO:1904355","count":2},{"id":"GO:0035994","count":2},{"id":"GO:0045444","count":2}]},{"hash":"592124631096631237","title":"Ribosome Biogenesis and Growth Signaling","description":"The prominent translation and ribosome biogenesis terms indicate a core protein synthesis module. Also present are cell growth and cell cycle terms, suggesting linkage to proliferation, while stress and telomere maintenance terms hint at regulatory coordination with nuclear integrity. Taken together, this cluster reflects ribosome assembly/translation connected to growth and stress signaling.","confidence":"Medium","size":15,"edges":8,"triangles":3,"max_degree":5,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0002181","count":3},{"id":"GO:0042254","count":3},{"id":"GO:2000727","count":2},{"id":"GO:0016049","count":2}]},{"hash":"948962132106770299","title":"DNA Damage Response and Chromatin Repair","description":"This cluster is dominated by GO terms related to DNA damage sensing and repair and chromatin-associated processes (mitotic G2 DNA damage checkpoint signaling, regulation of DSB repair via NHEJ, HR, and protein localization to chromatin; plus response to ionizing radiation), indicating proteins that coordinate DNA repair within chromatin context. Some developmental or structural terms present are likely secondary associations or annotation noise.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007095","count":2},{"id":"GO:2001032","count":1},{"id":"GO:0071168","count":1},{"id":"GO:1905168","count":1},{"id":"GO:0010212","count":1}]},{"hash":"443756475490908842","title":"mRNA decay and transcription regulation","description":"The Top Terms are dominated by mRNA metabolism processes (deadenylation-dependent decay, deadenylation-independent decapping, poly(A) tail shortening, and processing body assembly) along with transcription elongation by RNA polymerase II and its regulation. This points to a cohesive theme around mRNA stability and transcription control. A few terms related to development and pheromone response are present but appear as minor outliers. Overall, the cluster seems to group proteins involved in RNA turnover and transcription regulation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":1},{"id":"GO:0032968","count":1},{"id":"GO:0017148","count":1},{"id":"GO:0000289","count":1},{"id":"GO:0010606","count":1}]},{"hash":"2016285056192141053","title":"Unknown","description":"There are no shared GO terms or network connections (no edges, no triangles) to indicate a common function or pathway among the 15 proteins, so no interpretable label can be assigned. Unknown is the appropriate designation with no confidence.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1385815709829123790","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:2000587","count":1},{"id":"GO:0071475","count":1},{"id":"GO:0001560","count":1}]},{"hash":"849836408790867928","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006189","count":1},{"id":"GO:0044208","count":1},{"id":"GO:0038128","count":1},{"id":"GO:0050821","count":1},{"id":"GO:0000079","count":1}]},{"hash":"111886293511783883","title":"Organelle RNA processing and mitochondrial translation","description":"These proteins show strongest signals in organelle gene expression: regulation of mitochondrial translation, mitochondrial mRNA processing, and chloroplast RNA processing, suggesting a common theme of organelle RNA processing and translation. Other terms are more general regulatory or DNA repair processes and do not clearly redefine the main theme.","confidence":"Low","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070129","count":1},{"id":"GO:2000587","count":1},{"id":"GO:0071475","count":1},{"id":"GO:0001560","count":1},{"id":"GO:0006471","count":1}]},{"hash":"3684298016329683","title":"Transcription Regulation and Chromatin Modification","description":"The terms are dominated by regulation of transcription and chromatin state (e.g., negative regulation of transcription regulatory region DNA binding; regulation of histone acetylation and chromatin silencing). Although a couple of terms touch on cell migration or B cell differentiation, the strongest signal across the cluster is gene expression control through transcriptional regulation and chromatin modifications.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061408","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0007205","count":2},{"id":"GO:2001275","count":2},{"id":"GO:0051595","count":1}]},{"hash":"2131924351502312235","title":"Multifunctional Regulators of Trafficking, Signaling, and Transcription","description":"The top GO terms point to regulation across several cellular domains: membrane trafficking (receptor recycling, endosome size), cytoskeletal signaling (Rho pathway), neuronal signaling (glutamatergic synaptic transmission), and nuclear regulation (transcription, chromatin remodeling). This spread suggests a cluster of proteins that act as regulators across multiple processes rather than a single pathway, hence a label capturing their broad regulatory roles in trafficking, signaling, and transcription. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0001881","count":11},{"id":"GO:0051036","count":11},{"id":"GO:0035023","count":11},{"id":"GO:0035249","count":11},{"id":"GO:0006355","count":11}]},{"hash":"2156665642914994400","title":"Retroviral integration and proviral latency","description":"This cluster is dominated by terms related to genome integration and reverse-transcription processes (DNA integration, DNA recombination, RNA-templated DNA biosynthetic process) plus explicit references to viral entry into the host nucleus and establishment of proviral latency. Together these point to retroviral life cycle steps where a viral genome integrates into the host genome and may become latent. Some symbiont-related terms appear, but the clearest theme centers on proviral integration and latency.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0006310","count":1},{"id":"GO:0006278","count":1},{"id":"GO:0075732","count":1}]},{"hash":"2038899161157673012","title":"Redox Homeostasis and tRNA Modification","description":"The top GO terms strongly point to redox-related processes (cell redox homeostasis; Mo-molybdopterin cofactor biosynthesis supporting redox enzymes) and RNA modification (tRNA wobble thiolation and tRNA seleno-modification). While a few terms touch on development and differentiation, the dominant signals are redox maintenance and RNA modification, suggesting a cluster centered on redox-linked RNA processing activities.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":2},{"id":"GO:0021510","count":1},{"id":"GO:0035335","count":1},{"id":"GO:0002143","count":1},{"id":"GO:0018192","count":1}]},{"hash":"2281409040613116175","title":"Unknown","description":"The top GO terms cover a highly diverse mix: apoptosis regulation, phosphorylation signaling, visual perception, cell cycle transitions, general development, neural signaling (long-term potentiation, excitatory postsynaptic potential), heart development, and even plant ABA signaling. There is no single cohesive biological theme tying these proteins together, and the cluster has no edges, suggesting little functional cohesion. Therefore, Unknown with None confidence.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043065","count":2},{"id":"GO:0010800","count":2},{"id":"GO:0007601","count":2},{"id":"GO:0000278","count":2},{"id":"GO:0000086","count":2}]},{"hash":"1270333114664405585","title":"RNA and Protein Methylation Enzymes","description":"The proteins in this cluster are linked to several methylation-related GO terms, including peptidyl-lysine dimethylation, RNA guanine-N7 methylation, 7-methylguanosine mRNA capping, and rRNA modification, plus histone methylation in older annotations. There are also biosynthetic processes that can involve methyltransferases, such as biotin, polyamine, and vitamin E biosynthesis. Taken together, the common theme is methylation-based modification of RNA and proteins, suggesting these proteins function as methyltransferases or related modifiers.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0018027","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0009102","count":1},{"id":"GO:0006596","count":1}]},{"hash":"943631079746274600","title":"Actin-dependent vesicle transport and cytokinesis","description":"The top GO terms converge on actin-mediated movement and organization (vesicle transport along actin filaments, secretory granule localization) plus processes at the cell division boundary (membrane addition at cytokinesis, spindle orientation), indicating a theme of cytoskeletal remodeling coordinating trafficking and cytokinesis; additional terms like regulation of GTPase activity and VEGF-related migration support this actin/cytoskeleton-led functional ensemble.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902405","count":1},{"id":"GO:0031585","count":1},{"id":"GO:0030050","count":1},{"id":"GO:0038089","count":1},{"id":"GO:0032252","count":1}]},{"hash":"1833361165948221940","title":"DNA Damage Response and Stress Regulation","description":"This cluster centers on ubiquitination, UV/damage-responsive transcription and translation control, and apoptosis signaling, indicating a cohesive stress and DNA damage response program; peripheral terms like neurotransmitter transport and epithelial polarity are weaker signals.","confidence":"High","size":15,"edges":11,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0006836","count":2},{"id":"GO:0051260","count":2},{"id":"GO:2000372","count":2},{"id":"GO:0009408","count":2}]},{"hash":"1500067472338690517","title":"Autophagy and vacuolar targeting pathways","description":"The protein set is strongly enriched for autophagy- and vacuole-related processes, including macroautophagy, autophagosome assembly, and Cvt/microautophagy pathways, along with vesicle targeting to membranes. A single term about cerebellar neuron development is likely unrelated noise; overall, the cluster maps to autophagy and vacuolar trafficking.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990414","count":2},{"id":"GO:0000422","count":1},{"id":"GO:0051697","count":1},{"id":"GO:0006612","count":1},{"id":"GO:0045732","count":1}]},{"hash":"949782390245197752","title":"Chromatin Regulation and RNA-Mediated Silencing","description":"The Top Terms are dominated by chromatin- and transcription-related processes (histone mRNA catabolic process, apoptotic chromosome condensation, regulatory ncRNA-mediated gene silencing) with a spread into DNA repair and growth signaling. This suggests a cluster biased toward chromatin dynamics and RNA-based regulation of gene expression, even though some terms are obsolete or less connected.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071044","count":2},{"id":"GO:2000587","count":1},{"id":"GO:0071475","count":1},{"id":"GO:0001560","count":1},{"id":"GO:0006471","count":1}]},{"hash":"556878742451567252","title":"Plant Development and Hormone Signaling","description":"The cluster's GO terms are dominated by plant-specific developmental processes (seed development, floral meristem growth, multicellular organism development) and hormone signaling pathways (ABA- and ethylene-activated signaling; auxin-related pathway). There is also regulation of transcription and a defense-related term (response to chitin) that can connect to stress responses during development. Despite one rRNA processing term, the overall pattern points to a module of plant growth regulation and hormone-driven patterning.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006364","count":1},{"id":"GO:0060774","count":1},{"id":"GO:0048316","count":1},{"id":"GO:1901959","count":1},{"id":"GO:0009738","count":1}]},{"hash":"1921464627636740798","title":"Ubiquitin-Proteasome Regulation","description":"The top terms center on protein ubiquitination and SCF-dependent proteasomal degradation, suggesting a core theme around protein turnover and regulation by the ubiquitin-proteasome system. While there are ancillary terms related to RNA processing and other processes, the strongest signal comes from ubiquitination and proteolysis, with some indication of protein complex assembly via homooligomerization. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0000398","count":2},{"id":"GO:0006836","count":2},{"id":"GO:2000372","count":2},{"id":"GO:0016567","count":2}]},{"hash":"2026485712486411781","title":"DNA replication and repair machinery","description":"The dominant GO terms are related to DNA replication, mitotic checkpoint signaling, UV-damage excision repair, and translesion synthesis, suggesting the proteins cluster around DNA synthesis and damage tolerance/repair pathways. A few other terms (protein oligomerization, peroxisomal import, complex III assembly) may reflect broader roles in assembling multi-subunit complexes, but the core signal points to replication/repair functions.","confidence":"Medium","size":15,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":1},{"id":"GO:0016562","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0034214","count":1},{"id":"GO:0034551","count":1}]},{"hash":"891700556665667738","title":"DNA Replication and Damage Response","description":"This cluster's top GO terms are dominated by DNA replication (GO:0006260), cell division (GO:0051301), mitotic DNA replication checkpoint signaling (GO:0033314), and SOS response (GO:0009432), pointing to genome maintenance and DNA damage response as the core theme. Other terms such as viral genome replication, oxidative stress response, and intracellular trafficking appear as ancillary connections, but the dominant signal favors replication and damage-response processes.","confidence":"Medium","size":15,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0019079","count":7},{"id":"GO:0006260","count":7},{"id":"GO:0034599","count":6},{"id":"GO:0016558","count":6},{"id":"GO:0051301","count":6}]},{"hash":"1704006830504791056","title":"Unknown","description":"The top GO terms span diverse processes across neural development, immune signaling, metabolism, and stress responses, with no single unifying function, so no specific label fits.","confidence":"","size":15,"edges":103,"triangles":430,"max_degree":14,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016477","count":15},{"id":"GO:0010898","count":15},{"id":"GO:0060484","count":15},{"id":"GO:0022038","count":15},{"id":"GO:0050853","count":15}]},{"hash":"342930820710161013","title":"Calcium Transport and Membrane Excitability","description":"The cluster centers on calcium signaling and electrical activity, including high voltage-gated calcium channel\u2013driven calcium transport and regulation, as well as membrane depolarization in Purkinje/other excitable cells and related gastric secretion regulation. Developmental terms appear but the dominant trend is calcium-mediated signaling across tissues.","confidence":"Medium","size":15,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":3},{"id":"GO:0019233","count":3},{"id":"GO:0009636","count":2},{"id":"GO:2000114","count":2},{"id":"GO:0001890","count":2}]},{"hash":"1425820669415559436","title":"Lipid biosynthesis and membrane trafficking","description":"The top GO terms cluster around lipid metabolism (lipid A biosynthesis, mevalonate pathway/isoprenyl biosynthesis, sphingomyelin catabolism) and vesicle transport from the ER to the Golgi, suggesting a module focused on lipid production and membrane trafficking. Some terms also touch on cardiovascular development, which may reflect broader signaling contexts or annotation overlap, but the core theme appears lipid/membrane\u2013related. ","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009245","count":10},{"id":"GO:0000082","count":10},{"id":"GO:0001569","count":9},{"id":"GO:0016576","count":9},{"id":"GO:0035690","count":9}]},{"hash":"2228511062813335253","title":"Golgi sugar-nucleotide transporters","description":"Top GO terms include transmembrane transport of UDP-galactose into the Golgi lumen, UDP-GlcNAc transport, and sialic acid transport, suggesting a shared role in delivering sugar nucleotides into the Golgi for glycosylation. Other terms (DNA repair, apoptosis, plant development, immune regulation) appear ancillary or annotation-specific; the strongest signal is Golgi sugar-nucleotide transport, so this label best captures the cluster\u2019s core function.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033683","count":1},{"id":"GO:0036297","count":1},{"id":"GO:0033081","count":1},{"id":"GO:0006915","count":1},{"id":"GO:0097624","count":1}]},{"hash":"1469635077547078874","title":"Innate immune signaling and lipid metabolism","description":"The GO terms show strong signals for innate immunity (inflammatory response, TLR8 signaling, NF-kappaB activation) and ubiquitination, alongside lipid-related processes (sphingosine biosynthesis, fatty acid response, triglyceride catabolic process, acetylcholine metabolism), suggesting a cohesive theme of immune signaling intertwined with lipid metabolism.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0016567","count":3},{"id":"GO:0046512","count":3},{"id":"GO:0070542","count":3},{"id":"GO:0042346","count":2}]},{"hash":"971522374878023234","title":"Mitochondrial Transport and Energy Regulation","description":"The cluster shows strong representation of GO terms for transport across the mitochondrial membrane (ADP/ATP, alpha-ketoglutarate, magnesium) and regulation of mitochondrial membrane potential and permeability, all central to energy production. Additional terms related to insulin/IGF signaling and oxidative stress further tie the proteins to mitochondria-centered metabolic regulation, supporting a cohesive theme of mitochondrial transport and energy governance.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":4},{"id":"GO:0051881","count":4},{"id":"GO:0015742","count":4},{"id":"GO:0032869","count":4},{"id":"GO:1990314","count":4}]},{"hash":"67431276620594452","title":"Glycolysis and sugar metabolism","description":"Top GO terms point to glycolytic and sugar-enabled metabolic processes (glycolysis, fructose metabolism, carbohydrate phosphorylation, PPP flux, and serine biosynthesis), suggesting a cluster of proteins involved in central carbon metabolism and energy production from sugars. Dephosphorylation and cellular regulation terms imply control of metabolic flux. A few terms like brain development and cobalt ion response may reflect broader housekeeping or stress-related roles rather than core metabolism. Overall, the cluster is best described as glycolysis and sugar metabolism.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0016311","count":4},{"id":"GO:0007420","count":4},{"id":"GO:0006000","count":3},{"id":"GO:0046835","count":3},{"id":"GO:0043456","count":3}]},{"hash":"483042875551777836","title":"Neuronal development and synapse regulation","description":"This cluster\u2019s terms cluster most clearly around neural development and synaptic organization, with items like synapse organization and positive regulation of neuron apoptotic processes, plus Wnt signaling which is important in neural development. While there are a few outliers (e.g., cardiac development and chromatin-related processes), the dominant theme appears to be neuronal connectivity and growth. Confidence: Medium","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032461","count":1},{"id":"GO:1904808","count":1},{"id":"GO:0050821","count":1},{"id":"GO:0050808","count":1},{"id":"GO:0061051","count":1}]},{"hash":"1792392870102527374","title":"Zinc Ion Homeostasis and Transport","description":"The cluster is dominated by zinc-related terms: zinc import across the plasma membrane, detoxification and intracellular zinc homeostasis, and cellular responses to zinc ion starvation, suggesting a cohesive module centered on zinc handling. While there are a few outliers (ethanol metabolism, mitochondrial ribosome assembly, limb development), the zinc-associated terms provide the strongest common function tying these proteins together.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006067","count":2},{"id":"GO:0061668","count":2},{"id":"GO:0010312","count":1},{"id":"GO:0006831","count":1},{"id":"GO:0006830","count":1}]},{"hash":"175798620889645128","title":"Unknown","description":"The terms include dopamine and serotonin-related neurotransmitter metabolism, xenobiotic response, and various metabolic and developmental processes (thiamine and quinolinate biosynthesis, aluminum ion response, pituitary development), with several obsolete annotations. There is no consistent single theme or pathway tying these functions together, suggesting the cluster may group disparate processes rather than a coherent function.","confidence":"","size":15,"edges":13,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":6},{"id":"GO:0009228","count":5},{"id":"GO:0014063","count":5},{"id":"GO:0043046","count":5},{"id":"GO:0055114","count":5}]},{"hash":"1841185149171697552","title":"Symbiont-driven immune modulation","description":"The top terms point to antigen processing/presentation via MHC II, regulation of tolerance, and symbiont-mediated effects on host immune pathways, implying a theme of host immune modulation by symbiotic organisms. Some transcription regulation and glycosphingolipid biosynthesis terms appear, but the dominant signal centers on immune interaction with symbionts.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043433","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0001576","count":1},{"id":"GO:0036210","count":1},{"id":"GO:0051999","count":1}]},{"hash":"2255188466592496884","title":"Cardiac signaling with inflammation and pain cues","description":"The cluster includes terms linked to heart tissue communication (SA node to atrial cardiac muscle cell), inflammatory/chemokine production (macrophage inflammatory protein 1 alpha, chemokine production), NF-kappaB regulation, cell migration, and pain mechanism (detection of mechanical stimulus involved in sensory perception of pain), plus hepatocyte apoptosis. This suggests a theme of signaling and immune/pain responses that span cardiac and inflammatory pathways, rather than a single, tightly cohesive function. Given the mix and lack of strong direct overlap, this labeling is a best-effort representation rather than a definitive module.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086070","count":3},{"id":"GO:1903444","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0007253","count":3},{"id":"GO:0072660","count":3}]},{"hash":"498195802535146461","title":"Diverse membrane transport","description":"This cluster\u2019s top GO terms largely describe transport/export activities across membranes for various substrates (xenobiotics, daunorubicin, taurine, bacteriocins, oligopeptides, ceramide, peroxisomal fatty acids, teichoic acid), suggesting a common theme of transporter or membrane trafficking functions. An outlier term (nucleotide-excision repair) exists, indicating some annotation noise, but overall the shared theme is membrane transport. Given no interaction edges, the label reflects a broad transport-related grouping rather than a single precise pathway.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046618","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0015910","count":2},{"id":"GO:0015777","count":2},{"id":"GO:0043213","count":2}]},{"hash":"2049461846779461234","title":"Transmembrane Transport and Proteoglycan Metabolism","description":"This cluster centers on membrane transport functions (transmembrane, sodium, carbohydrate transport) and glycosaminoglycan-related processes (heparan and dermatan sulfate proteoglycan biosynthesis and metabolism). The presence of development-related terms (chondrocyte development, ureteric bud formation) can be linked to ECM proteoglycan roles in morphogenesis. Overall, the proteins seem to co-cluster around transport activities intertwined with extracellular matrix glycosaminoglycan synthesis/modification and related developmental contexts.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055085","count":1},{"id":"GO:0006814","count":1},{"id":"GO:0008643","count":1},{"id":"GO:0002063","count":1},{"id":"GO:0015014","count":1}]},{"hash":"1351442408024145876","title":"Muscle and heart development","description":"Most of the top GO terms describe processes in muscle and heart formation and development (cardiac ventricle development; smooth muscle tissue development; negative regulation of skeletal muscle cell differentiation). While a few terms touch on DNA repair or reproductive biology, the dominant signal points to musculoskeletal cardiovascular morphogenesis and differentiation, justifying the label. The obsolete terms are likely annotation artifacts and do not define the cluster's core theme.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:1990166","count":1},{"id":"GO:0008585","count":1},{"id":"GO:2000721","count":1},{"id":"GO:0048745","count":1}]},{"hash":"142415907584816867","title":"Plant cell wall biosynthesis and glycosylation","description":"These proteins cluster around plant cell wall construction: enriched terms include homogalacturonan and glucuronoxylan biosynthesis, mucilage production, and plant-type secondary cell wall biogenesis, indicating pectin/hemicellulose synthesis and wall assembly. Glycosylation-related GO terms support wall protein modification, while sugar metabolism terms reflect the carbohydrate supply for wall components. The skeletal muscle regeneration term appears as noise; overall the theme is plant cell wall biosynthesis and glycosylation.","confidence":"High","size":15,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":8},{"id":"GO:0016266","count":6},{"id":"GO:0010192","count":4},{"id":"GO:0010289","count":4},{"id":"GO:0010417","count":4}]},{"hash":"527603095756549421","title":"Diverse biosynthesis and methylation functions","description":"These proteins touch several biosynthetic pathways (biotin, menaquinone, antibiotic biosynthesis) and multiple methylation reactions (rRNA methylation, N-terminal peptidyl-glycine methylation, peptidyl-lysine dimethylation). There is no single cohesive pathway, but the common theme appears to be metabolic biosynthesis alongside post-translational methylation activities.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":2},{"id":"GO:2000124","count":2},{"id":"GO:0006212","count":2},{"id":"GO:0009234","count":2},{"id":"GO:0055114","count":2}]},{"hash":"1331928860741207066","title":"Regulation of ubiquinone biosynthesis and lipid homeostasis","description":"The top GO terms point to regulatory processes in coenzyme Q (ubiquinone) biosynthesis and lipid homeostasis, with related hints at tocopherol (vitamin E) pathway regulation and broader metabolic signaling (glycogen metabolism, autophagy, kinase activity). This suggests a cohesive theme around metabolic regulation of lipid-derived cofactors rather than a single, narrowly defined function, justifying a label focused on ubiquinone/lipid biosynthesis regulation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901006","count":3},{"id":"GO:0010795","count":3},{"id":"GO:0055088","count":3},{"id":"GO:0021692","count":3},{"id":"GO:1902171","count":3}]},{"hash":"620557544514540503","title":"Neuroinflammation and cytokine regulation","description":"This cluster centers on inflammatory signaling and cytokine production, highlighted by terms for NLRP3 inflammasome assembly, IL-1\u03b2 production, and regulation of IL-2. It also includes defense against protozoan pathogens and intracellular signaling, with brain development and Golgi organization suggesting neural context and cytokine trafficking roles. Overall, a coherent theme is neuroinflammatory signaling with cytokine regulation rather than a single metabolic pathway.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0035556","count":2},{"id":"GO:1900227","count":1},{"id":"GO:1900017","count":1}]},{"hash":"1708968708744736834","title":"Plant Cell Wall Biosynthesis and Glycosylation","description":"The top GO terms are centered on plant cell wall polysaccharide biosynthesis (mucilage, pectin, xylan, secondary cell wall biogenesis) and on protein O-linked glycosylation, indicating a cluster of plant cell wall\u2013associated polysaccharide synthesis and glycoproteins. Some terms (e.g., glycogen biosynthesis) may reflect annotation noise, but the dominant signal ties to plant cell wall construction and glycosylation.","confidence":"High","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010192","count":1},{"id":"GO:0010289","count":1},{"id":"GO:0010417","count":1},{"id":"GO:0043403","count":1},{"id":"GO:0071555","count":1}]},{"hash":"966571234204320516","title":"Unknown","description":"The terms are highly heterogeneous: immune signaling (type I interferon response), steroid receptor\u2013related processes, sexual differentiation and prostate development, and bacterial cell wall/lipid biosynthesis. With no single dominant function or pathway and no network connectivity, there isn\u2019t a coherent theme to bind these proteins into a meaningful, specific label.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019878","count":2},{"id":"GO:0071357","count":2},{"id":"GO:0006463","count":2},{"id":"GO:0046661","count":2},{"id":"GO:0030850","count":2}]},{"hash":"1096474538083289466","title":"HGF/c-Met Signaling","description":"This cluster\u2019s top terms center on hepatocyte growth factor: cellular response to hepatocyte growth factor stimulus and hepatocyte growth factor receptor signaling pathway, indicating a link to HGF/c-Met signaling. However, many other terms are unrelated or obsolete, and there are no edges connecting the proteins, so the association is weak and likely noisy.","confidence":"Low","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0035729","count":2},{"id":"GO:0048012","count":2},{"id":"GO:1902348","count":1},{"id":"GO:0019260","count":1}]},{"hash":"1081893051994992905","title":"Unknown","description":"Unknown","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0006469","count":4},{"id":"GO:0007568","count":4},{"id":"GO:0061158","count":3},{"id":"GO:0010875","count":3}]},{"hash":"1925989350991947401","title":"Unknown","description":"The GO terms are highly diverse (development, epithelial differentiation, cell cycle, metabolism, and multiple RNA modification pathways) with no clear shared function or pathway linking the proteins. This lack of a cohesive theme makes a meaningful, specific label inappropriate.","confidence":"","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":1},{"id":"GO:0035335","count":1},{"id":"GO:0002143","count":1},{"id":"GO:0018192","count":1},{"id":"GO:0030855","count":1}]},{"hash":"938294352371338310","title":"RNA Modification and Methylation","description":"Dominant signal is RNA modification and methylation: RNA guanine-N7 methylation, mRNA capping, tRNA wobble uridine modification, and protein arginine methylation. Depalmitoylation and some metabolic terms appear peripheral, with nodulation and tellurium response likely annotation noise. Therefore, label emphasizes RNA modification/methylation.","confidence":"Medium","size":15,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006596","count":2},{"id":"GO:0002084","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0009877","count":2},{"id":"GO:0006370","count":2}]},{"hash":"526229467789193518","title":"Mitotic Ubiquitination and Proteasomal Degradation","description":"The cluster centers on ubiquitin-related processes (autoubiquitination, SCF-dependent proteasomal degradation, ERAD) and mitotic cell cycle events (G2/M transition, exit from mitosis, chromosome segregation), indicating a cohesive role of ubiquitin-proteasome\u2013mediated protein turnover in mitosis. Peripheral terms like viral process or synapse assembly are less representative of the core function. ","confidence":"High","size":14,"edges":89,"triangles":341,"max_degree":13,"top_function":"chromosome segregation","top_go_terms":[{"id":"GO:0051865","count":13},{"id":"GO:0030433","count":13},{"id":"GO:0070911","count":13},{"id":"GO:0031146","count":12},{"id":"GO:0007059","count":12}]},{"hash":"1528614417667798512","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":49,"triangles":83,"max_degree":11,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060044","count":11},{"id":"GO:0030216","count":11},{"id":"GO:0090263","count":11},{"id":"GO:0035329","count":11},{"id":"GO:0006915","count":11}]},{"hash":"1783168627151891878","title":"Unknown","description":"The top GO terms are highly diverse: transcriptional regulation, chemotaxis and cell migration, multiple tissue development terms (lung mesenchyme, corpus callosum), B cell receptor signaling, apoptosis, amino acid starvation response, and viral response. There isn\u2019t a single cohesive biological process linking these terms, so a concise, representative label cannot be determined. ","confidence":"","size":14,"edges":12,"triangles":2,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":13},{"id":"GO:0006935","count":13},{"id":"GO:0016477","count":12},{"id":"GO:0010898","count":12},{"id":"GO:0060484","count":12}]},{"hash":"1418573840306571056","title":"Ubiquitin-Driven Proteostasis and ERAD","description":"The top GO terms are dominated by ubiquitination and ubiquitin-dependent ERAD-related processes (K63-linked ubiquitination, autoubiquitination, ERAD pathway), pointing to a protein cohort focused on regulated protein turnover and quality control. Some terms also touch on stress-responsive regulation (ethanol response, glucocorticoid metabolism, chaperone assembly), suggesting proteostasis is modulated under diverse stress conditions.","confidence":"High","size":14,"edges":13,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":14},{"id":"GO:0051865","count":14},{"id":"GO:0030433","count":14},{"id":"GO:0090035","count":13},{"id":"GO:0071361","count":13}]},{"hash":"1989077300926848047","title":"Chemical stress and detoxification response","description":"This cluster is enriched for GO terms related to responding to a wide range of chemicals and stressors, including xenobiotics, ethanol, metals (selenium, aluminum), lipopolysaccharide, and herbicides, suggesting a shared role in chemical stress sensing and detoxification. The presence of protein modification and repair terms indicates maintenance of proteostasis under stress, while porphyrinogen IX biosynthesis hints at linked redox/metabolic processes. Overall, the proteins appear coordinated around chemical stress response and detoxification pathways, with some metabolic context. ","confidence":"Medium","size":14,"edges":14,"triangles":6,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0042493","count":4},{"id":"GO:0045471","count":4},{"id":"GO:0010269","count":4},{"id":"GO:0032496","count":4}]},{"hash":"445699619275274472","title":"Ubiquitin-Proteasome Regulation of Cell Cycle","description":"The cluster shows strong enrichment for ubiquitin-dependent protein catabolic processes and protein polyubiquitination, centered on SCF/ proteasome pathways, plus links to DNA replication initiation and G1/S checkpoint signaling. This suggests a cohesive module where ubiquitin-mediated protein turnover governs cell-cycle progression and related stress responses.","confidence":"High","size":14,"edges":8,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":5},{"id":"GO:1902564","count":5},{"id":"GO:0042752","count":4},{"id":"GO:0000083","count":4},{"id":"GO:1902916","count":4}]},{"hash":"2007770420087069282","title":"Unknown","description":"The top GO terms span diverse areas from poly-ADP-ribosylation and transcriptional regulation to cardiac communication, adipogenesis, cell migration, NF-kB signaling, membrane localization, inflammatory cytokine production, and mechanosensory pain detection. There is no single cohesive process tying these together, suggesting the cluster does not reflect one unified function but rather a mix of unrelated roles, so a specific label cannot be confidently assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070212","count":6},{"id":"GO:0000083","count":6},{"id":"GO:0086070","count":5},{"id":"GO:1903444","count":5},{"id":"GO:0016477","count":5}]},{"hash":"1666287159843592542","title":"Energy metabolism and redox homeostasis","description":"This cluster centers on core energy production and antioxidant balance: glycolytic process, pyruvate biosynthesis, and leucine catabolism point to carbohydrate- and amino-acid-derived energy; glutathione biosynthesis and cell redox homeostasis indicate oxidative stress management during metabolism; response to starvation and liver development terms further align with metabolic adaptability and hepatic metabolic roles.","confidence":"High","size":14,"edges":7,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0006552","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0009097","count":3},{"id":"GO:0006096","count":3},{"id":"GO:0045454","count":3}]},{"hash":"174647699807568135","title":"Striatum development and morphine response","description":"The top GO terms are dominated by neural context: striatum development and response to morphine, suggesting a cluster of proteins involved in brain development and opioid signaling. Other terms point to general cellular processes (centrosome-associated microtubule anchoring, histone modification) and immune response, which are less specific to this neural theme. Overall, the strongest coherent signal is neuronal development and morphine responsiveness, giving a moderate confidence in this label.","confidence":"Medium","size":14,"edges":54,"triangles":80,"max_degree":10,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043278","count":4},{"id":"GO:0006478","count":3},{"id":"GO:0034454","count":3},{"id":"GO:0021756","count":3},{"id":"GO:0051348","count":3}]},{"hash":"1302361254398457849","title":"ER Proteostasis and Heat Stress Response","description":"This cluster is dominated by terms tied to maintaining protein homeostasis under stress: protein folding in the ER, response to unfolded protein, ER-associated quality control, and proteasome-mediated nuclear quality control, alongside redox homeostasis and heat response. The presence of translation frameshifting and protein oligomerization suggests broader connections to protein synthesis and assembly under stress. Some terms (DNA replication, a developmental signaling term) may reflect multi-functional proteins or incidental associations, but the core theme is proteostasis during heat/ER stress.","confidence":"Medium","size":14,"edges":11,"triangles":2,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0009408","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1900035","count":2},{"id":"GO:1901621","count":2}]},{"hash":"2083448365514158812","title":"Ribosome Biogenesis and RNA Processing","description":"This cluster is dominated by terms for rRNA maturation, ribosomal subunit assembly (including mitochondrial large subunit), ribosome biogenesis, and RNA processing steps such as exon ligation and spliceosome-mediated splicing, plus stress granule localization. A single DNA replication term is present but the core signal is nucleolar/RNA metabolism and protein assembly into ribosomes.","confidence":"High","size":14,"edges":30,"triangles":22,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":9},{"id":"GO:1903608","count":8},{"id":"GO:0000462","count":8},{"id":"GO:1902775","count":8},{"id":"GO:0000463","count":8}]},{"hash":"1236330914703983599","title":"Unknown","description":"The top GO terms indicate multiple, largely unrelated cellular processes\u2014secretory trafficking (ER to Golgi), DNA replication, mRNA splicing, histone dephosphorylation, and various stress or metabolic responses (xenobiotic response, mevalonate pathway regulation, sphingomyelin catabolism, and cardiac hypertrophy). The lack of a single dominant functional theme across the cluster means there isn\u2019t a coherent, well-defined label beyond Unknown.","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006888","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0070262","count":3},{"id":"GO:0001569","count":2}]},{"hash":"904657826567481906","title":"Embryonic Organogenesis and Neural Development","description":"The cluster shows strong signals for developmental processes such as heart development, cranial skeleton morphogenesis, and angiogenesis, along with neural-activity terms like synaptic potentiation and visual perception. Together these point to vertebrate embryogenesis involving neural and vascular tissue formation and maturation, with some general cellular processes as background. An outlier plant signaling term is present, but the dominant theme remains embryonic organ formation with neural components.","confidence":"High","size":14,"edges":8,"triangles":2,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":10},{"id":"GO:0048701","count":8},{"id":"GO:0060291","count":6},{"id":"GO:0007507","count":6},{"id":"GO:0043065","count":6}]},{"hash":"598963601784392566","title":"Unknown","description":"The proteins are linked to a highly diverse mix of processes (histone catabolic and ubiquitination, actin/cytoskeleton organization, septin ring and septation signaling, NF-kappaB and Wnt signaling, and dosage compensation) with no shared, cohesive function or network structure, so a single interpretable label cannot be assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036205","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0090337","count":1},{"id":"GO:0032186","count":1},{"id":"GO:0090073","count":1}]},{"hash":"1063044354341266884","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is led by ubiquitination-related GO terms (autoubiquitination, K6-linked ubiquitination, ubiquitin-dependent ERAD, N-end rule), indicating proteins primarily function in tagging substrates for degradation via the ubiquitin-proteasome system. A few additional terms (histone catabolic process, isotype switching, signaling regulation) may reflect related ubiquitin-signaling roles or incidental associations, but the dominant theme is ubiquitin-mediated protein turnover.","confidence":"High","size":14,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":2},{"id":"GO:0085020","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0071596","count":2},{"id":"GO:0036205","count":1}]},{"hash":"1826890615718889447","title":"Unknown","description":"The cluster contains both DNA replication and SOS response terms but also a set of diverse transport processes (teichoic acid, bacteriocin, taurine, cobalt, vitamin, pheromone export, and ER-Golgi\u2013like transport). The lack of a single cohesive function linking these terms makes it unclear to assign a specific, representative label.","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0009432","count":5},{"id":"GO:0006888","count":4},{"id":"GO:0015777","count":4},{"id":"GO:0043213","count":4}]},{"hash":"1019771010131376082","title":"Ubiquitin-dependent degradation and signaling regulation","description":"This cluster shows a clear enrichment for ubiquitin-related processes: protein ubiquitination, autoubiquitination, and ubiquitin-dependent protein catabolic processes, along with Wnt receptor catabolic activity. These point to ubiquitin-proteasome\u2013mediated turnover that modulates signaling pathways (e.g., Wnt, TLR signaling) and cell-cycle\u2013related regulation, including growth control. Although some terms are obsolete, the dominant theme centers on ubiquitin-driven regulation of protein stability and signaling.","confidence":"High","size":14,"edges":25,"triangles":25,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0042787","count":1},{"id":"GO:0046621","count":1},{"id":"GO:0000209","count":1}]},{"hash":"1839843532560349575","title":"RNA processing and translation","description":"Most of the top terms converge on RNA biology: cytoplasmic translation and initiation (translation initiation, preinitiation complex formation, SSU-rRNA maturation), RNA processing (spliceosome-mediated alternative splicing, siRNA processing), and general RNA metabolism. A couple of terms (molting cycle, phosphatidylcholine biosynthesis) seem incidental and do not define the core function. Therefore, the label RNA processing and translation captures the central theme of RNA maturation and protein synthesis machinery.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018996","count":1},{"id":"GO:0043050","count":1},{"id":"GO:0002181","count":1},{"id":"GO:0001731","count":1},{"id":"GO:0000462","count":1}]},{"hash":"1277822441403467238","title":"Unknown","description":"The GO terms cover a mix of biosynthetic and catabolic pathways (ectoine, verruculogen, heptose, glycogen, fatty acids) and a sucrose response, with very little connectivity pointing to a single function. This lack of a cohesive theme and sparse edges make a precise label inappropriate.","confidence":"","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0097171","count":2},{"id":"GO:0009744","count":2},{"id":"GO:0005978","count":2},{"id":"GO:0097089","count":1}]},{"hash":"2172025096226964618","title":"Unknown","description":"The top GO terms span very diverse and sometimes unrelated processes (ion transport regulation, apoptotic and differentiation processes in animals, floral organ abscission in plants, acrosome assembly, spermatid differentiation, mammary gland proliferation, vesicle trafficking). There is no clear, single biological theme tying these proteins together, and annotations cross kingdoms, so a cohesive function cannot be inferred from the cluster. ","confidence":"","size":14,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1902307","count":2},{"id":"GO:0033028","count":2},{"id":"GO:1902647","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0097212","count":2}]},{"hash":"780582735549990214","title":"ER stress and heat-shock response","description":"This cluster is dominated by GO terms for protein folding in the endoplasmic reticulum, responses to heat and unfolded proteins, and negative regulation of heat-responsive signaling, indicating a coherent role in ER\u2013associated protein quality control and heat shock pathways. There are auxiliary terms related to broader cellular regulation (protein kinase activity, oligomerization) and some general processes (DNA replication, frameshifting) that may reflect housekeeping functions, but the core theme centers on stress-related protein folding and ER quality control.","confidence":"Medium","size":14,"edges":3,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":9},{"id":"GO:0009408","count":8},{"id":"GO:0006260","count":8},{"id":"GO:1900035","count":8},{"id":"GO:1901621","count":8}]},{"hash":"1450845975209987680","title":"DNA damage checkpoints and chromatin regulation","description":"These proteins are annotated with terms centered on DNA damage checkpoint signaling in mitosis and meiosis (intra-S, G1, meiotic recombination checkpoint) and on chromatin regulation (subtelomeric heterochromatin formation, histone H3-K79 methylation), suggesting a function in coordinating cell cycle progression with chromatin state. A few terms also reference RNA processing in organelles (chloroplast/mitochondrial), which may reflect peripherally related roles or annotation quirks rather than a cohesive organelle-specific function. Overall, the cluster most plausibly reflects DNA damage response coordination with chromatin regulation.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000677","count":1},{"id":"GO:0031573","count":1},{"id":"GO:1901259","count":1},{"id":"GO:0044783","count":1},{"id":"GO:0006348","count":1}]},{"hash":"444566652513319213","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045040","count":1},{"id":"GO:0030150","count":1},{"id":"GO:0071441","count":1},{"id":"GO:0001178","count":1},{"id":"GO:0071894","count":1}]},{"hash":"1290814456653541025","title":"RNA Methylation and tRNA Modification","description":"The top GO terms cluster around methylation and RNA modification: 7-methylguanosine mRNA capping, RNA (guanine-N7)-methylation, and tRNA wobble uridine modification, plus peptidyl-arginine methylation, suggesting a shared function in methyltransferase activities affecting RNA and proteins. Some other terms (biotin/antibiotic biosynthesis, nodulation, xenobiotic response) appear peripheral/noise given the lack of network connectivity (no edges), so the label focuses on the strongest common theme. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006370","count":2},{"id":"GO:0009102","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0046690","count":2},{"id":"GO:0009877","count":2}]},{"hash":"917063954711037443","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000027","count":1},{"id":"GO:0000350","count":1},{"id":"GO:0000387","count":1},{"id":"GO:0000389","count":1}]},{"hash":"57091633792721091","title":"ER-Golgi Vesicle Transport","description":"The cluster's GO terms are dominated by protein transport, notably ER-to-Golgi vesicle transport and retrograde endosome-to-Golgi trafficking, pointing to a cohesive theme of the secretory pathway. A few terms relate to transcription/translation and stress responses, suggesting additional cellular stress links, but the strongest signal is trafficking within the ER-Golgi system.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015031","count":1},{"id":"GO:0042147","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0031564","count":1},{"id":"GO:0010590","count":1}]},{"hash":"1215290367740583262","title":"Heat-shock proteostasis and protein folding","description":"This cluster is dominated by GO terms tied to heat response and proteostasis, including response to heat, unfolded protein response, ER protein folding, and nuclear ubiquitin-proteasome\u2013mediated quality control, plus protein complex oligomerization. Together, these indicate a theme of maintaining protein integrity under heat stress, i.e., a heat-shock proteostasis signature. A single unrelated term like DNA replication is likely incidental among the set. ","confidence":"High","size":14,"edges":6,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":9},{"id":"GO:0006260","count":9},{"id":"GO:1900035","count":9},{"id":"GO:1901621","count":9},{"id":"GO:0034975","count":9}]},{"hash":"1804408888267470902","title":"Peroxisome Biogenesis and Protein Import","description":"The cluster\u2019s top GO terms are dominated by peroxisome-related processes (ER-dependent peroxisome organization, protein import into peroxisome membrane/matrix, and peroxisome membrane biogenesis), indicating a shared function in peroxisome assembly and protein trafficking. A few unrelated terms appear but are sparse, so the main theme remains peroxisome biogenesis.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032581","count":1},{"id":"GO:0045046","count":1},{"id":"GO:0048137","count":1},{"id":"GO:0022615","count":1},{"id":"GO:0016558","count":1}]},{"hash":"407235497882404306","title":"Membrane-targeting and protein localization","description":"This cluster is dominated by GO terms related to targeting and translocation of proteins to membranes (ER/plasma membrane) and regulation of phospholipid movement, suggesting roles in membrane trafficking or localization. A few terms about development or host-symbiont protein modification are present but appear as noise, so the label captures the core membrane-associated theme without implying a single developmental or immune function.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048316","count":1},{"id":"GO:0098709","count":1},{"id":"GO:0051515","count":1},{"id":"GO:0031204","count":1},{"id":"GO:0061091","count":1}]},{"hash":"1099879558010145373","title":"Mitochondrial Transport and Membrane Potential Regulation","description":"The cluster\u2019s top GO terms center on transport of metabolites across mitochondrial membranes (ADP/ATP, alpha-ketoglutarate), and regulation of mitochondrial membrane permeability and membrane potential, with related processes like magnesium export and ATP transmembrane transport. The insulin and insulin-like growth factor\u2013related responses and fatty acid response fit within mitochondrial metabolic regulation, supporting a cohesive mitochondrial energy/transport function for the group.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070542","count":5},{"id":"GO:0046902","count":4},{"id":"GO:0051881","count":4},{"id":"GO:0015742","count":4},{"id":"GO:0032869","count":4}]},{"hash":"566107994769804624","title":"Nuclear RNA Processing and Transcription","description":"The GO terms show strong emphasis on nuclear RNA maturation and processing\u2014maturation of SSU-rRNA, tRNA processing, histone mRNA metabolism, and mRNA splicing via spliceosome\u2014as well as RNA Pol II transcription termination and nuclear import. P-body assembly and general RNA regulation further support a role in RNA metabolism and gene-expression control. While a couple terms are broader (hair cycle, stress response), the dominant theme is RNA maturation and transcription regulation in the nucleus.","confidence":"High","size":14,"edges":26,"triangles":30,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0042633","count":5},{"id":"GO:0051170","count":5},{"id":"GO:0030490","count":5},{"id":"GO:0008033","count":5},{"id":"GO:0008334","count":5}]},{"hash":"1354965089676387473","title":"Unknown","description":"The GO terms span neural apoptosis, cell cycle/DNA repair, spleen development, immune hypermutation, and broad stress responses, with no single dominant function tying the proteins; there is no cohesive theme evident (Edges/Triangles are zero).","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051402","count":1},{"id":"GO:1990506","count":1},{"id":"GO:0006286","count":1},{"id":"GO:0048536","count":1},{"id":"GO:0048872","count":1}]},{"hash":"536098469892474471","title":"Developmental Signaling and Cell Migration","description":"The cluster is enriched for development-related terms (root development, cell migration) and signaling/regulation processes (negative regulation of Wnt signaling, positive regulation of GTPase activity, positive regulation of core promoter binding), suggesting a shared role in developmental signaling and cellular movement. Some terms point to tissue-specific contexts like cardiac conduction, and vesicle trafficking, but the overarching theme aligns with development and migration rather than a single precise pathway.","confidence":"Medium","size":14,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":5},{"id":"GO:0090090","count":5},{"id":"GO:0043065","count":5},{"id":"GO:0048364","count":5},{"id":"GO:0043547","count":5}]},{"hash":"143853944151607014","title":"Unknown","description":"The top GO terms cover a wide range of biology\u2014from cell division and DNA-related localization to sex hormone metabolism, gonad development, Wnt signaling, and various stress responses. There isn\u2019t a single coherent function connecting these terms, so no clear, representative label can be assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:1990166","count":2},{"id":"GO:0008209","count":2},{"id":"GO:0008210","count":2},{"id":"GO:1904646","count":2}]},{"hash":"1066938597775478449","title":"DNA replication and protein folding/trafficking","description":"The top GO terms indicate a focus on DNA replication and mitotic checkpoint signaling, alongside several terms related to protein folding, unfolding, chaperone activity, and trafficking between ER/Golgi and mitochondria. This suggests a cluster that spans replication machinery with protein quality control and transport processes, hence a combined label that captures both themes.","confidence":"Medium","size":14,"edges":8,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0034214","count":3},{"id":"GO:0033314","count":3},{"id":"GO:0016310","count":3},{"id":"GO:0006888","count":3}]},{"hash":"414829631018940793","title":"Plant cell wall and carbohydrate biosynthesis","description":"This cluster shows a concentration of biosynthetic processes for carbohydrates and glycosphingolipids (globo- and IPC-related), pectin (rhamnogalacturonan II), starch, and sugar metabolism, coupled with cell wall organization and root hair development, pointing to plant cell wall assembly and carbohydrate metabolism as the common theme. Some terms (e.g., bacillithiol biosynthesis) are outliers, but the dominant signal supports a plant-centric biosynthesis/function cluster.","confidence":"Medium","size":14,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001576","count":2},{"id":"GO:0036210","count":2},{"id":"GO:0051999","count":2},{"id":"GO:0071555","count":2},{"id":"GO:0010306","count":2}]},{"hash":"1351071037199315610","title":"Branched-chain amino acid biosynthesis and related metabolism","description":"The cluster\u2019s prominent GO terms center on the biosynthesis and turnover of branched-chain amino acids (leucine, isoleucine, valine) and related D-amino acid metabolism, suggesting a cohesive theme around amino acid production and catabolism. Additional terms for UDP-L-arabinose and folic acid biosynthesis indicate broader biosynthetic activity, with a touch of transcriptional regulation via nitrogen catabolite repression. Overall, the dominant signal links to branched-chain amino acid pathways.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009098","count":1},{"id":"GO:0046656","count":1},{"id":"GO:0010817","count":1},{"id":"GO:0009097","count":1},{"id":"GO:0009099","count":1}]},{"hash":"225903123485081307","title":"Vacuolar transport and autophagy cluster","description":"This cluster\u2019s top GO terms are dominated by vacuolar transport, vacuole fusion (non-autophagic), and microautophagy, suggesting proteins involved in vacuole dynamics and autophagic pathways. There are a few outlier terms (polyphosphate biosynthesis, boron/borate transport, cell polarity regulation, locomotory behavior) that don\u2019t fit as neatly, but the strongest signal points to vacuole-related trafficking and autophagy. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006799","count":1},{"id":"GO:0007034","count":1},{"id":"GO:2000769","count":1},{"id":"GO:0048016","count":1},{"id":"GO:0016237","count":1}]},{"hash":"1501192632470171816","title":"Mesodermal differentiation and vasculogenesis","description":"The top GO terms cluster around mesodermal cell differentiation, erythrocyte development, and vasculogenesis, with links to regulation of stem cell differentiation and Notch signaling, plus blastocyst formation. This points to an integrated developmental program governing mesoderm-derived tissue formation and vascular/hematopoietic lineages, with regulatory processes suggesting transcriptional control during early development. Hence, a label emphasizing mesodermal differentiation and vascular development fits well.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048333","count":3},{"id":"GO:0048821","count":2},{"id":"GO:2001214","count":2},{"id":"GO:0061428","count":2},{"id":"GO:0045746","count":2}]},{"hash":"1528527508599722069","title":"Endosomal trafficking and mitochondrial metabolism","description":"This cluster\u2019s top GO terms center on vesicle trafficking and endosome organization (endosome organization, endocytic recycling) and mitochondrial-related processes (intracellular distribution of mitochondria, mitochondrial electron transport). While some terms are more peripheral, the strongest, recurring theme links endosomal handling with mitochondrial function, suggesting proteins coordinating trafficking with energy/metabolic aspects. Confidence: Medium","confidence":"","size":14,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007032","count":2},{"id":"GO:0032456","count":2},{"id":"GO:0048312","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0010725","count":2}]},{"hash":"1695848346932781026","title":"Ubiquitin-regulated immune signaling proteins","description":"This cluster centers on immune signaling processes (B cell receptor signaling, T cell differentiation) and ubiquitination regulation (K33-linked ubiquitination, negative regulation of protein ubiquitination), suggesting proteins that link ubiquitin signaling to adaptive immunity. A couple of outliers (sarcomere/muscle development, phototropism, distal tubule morphogenesis) are present but do not overwhelm the core theme.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990390","count":2},{"id":"GO:0050853","count":2},{"id":"GO:0043380","count":2},{"id":"GO:0031397","count":2},{"id":"GO:0045214","count":2}]},{"hash":"2257261328109437021","title":"Unknown","description":"The listed GO terms span development, sensory perception, stress responses, vascular regulation, and host-microbe interactions, with no single cohesive theme tying them together, so no confident functional label can be assigned.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033599","count":1},{"id":"GO:0045444","count":1},{"id":"GO:0007605","count":1},{"id":"GO:0008631","count":1},{"id":"GO:0010332","count":1}]},{"hash":"1622408440914099917","title":"Neuronal signaling and protein modification","description":"This cluster centers on GO terms tied to neuronal signaling (neurotransmitter transport, regulation of endocannabinoid signaling) and protein-level regulation (ubiquitination, homooligomerization, N-glycan processing). The co-occurrence of lipid metabolism and membrane-remodeling terms (acyl-chain remodeling, phosphatidylcholine catabolic processes, endocannabinoid regulation) suggests a theme of signaling at neuronal membranes with post-translational regulation. Confidence: Medium","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006836","count":5},{"id":"GO:0051260","count":5},{"id":"GO:2000372","count":5},{"id":"GO:0016567","count":5},{"id":"GO:0006491","count":2}]},{"hash":"1785181331361573019","title":"Cell Cycle Regulation & DNA Repair","description":"The top GO terms converge on cell cycle control (G1/S transition, CDK activity regulation, general cell cycle) with supportive themes in DNA repair, oxidative stress response, and proteasomal protein turnover, plus tyrosine dephosphorylation. This points to a cluster of proteins coordinating cell division with genome maintenance and related regulatory processes.","confidence":"Medium","size":14,"edges":82,"triangles":269,"max_degree":13,"top_function":"DNA repair","top_go_terms":[{"id":"GO:0035335","count":9},{"id":"GO:0007049","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0034599","count":3},{"id":"GO:0006281","count":3}]},{"hash":"1781879432961324737","title":"Bacterial methylation and biosynthesis enzymes","description":"This cluster is dominated by GO terms for various methylation reactions\u2014RNA methylation, rRNA methylation, peptidyl methylation, mRNA capping, and guanine-N7 methylation\u2014along with biosynthetic processes like cobalamin and antibiotic biosynthesis, all characteristic of bacterial methyltransferases and biosynthetic enzymes. Some terms (e.g., nodulation, tellurium ion response) are peripheral, but the central pattern supports a function tied to methylation and related biosynthetic pathways in bacteria.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":5},{"id":"GO:0018027","count":4},{"id":"GO:0031167","count":4},{"id":"GO:0006370","count":3},{"id":"GO:0036265","count":3}]},{"hash":"2151329363998061917","title":"Unknown","description":"The top GO terms are very diverse, covering nodulation, xenobiotic export, pigment biosynthesis, suberin biosynthesis, DNA repair, peroxisomal fatty acid import, teichoic acid and phospholipid transport, and bacteriocin transport/immunity. There is no single cohesive function or pathway uniting these terms, and the lack of edges/triangles suggests the cluster is not functionally cohesive.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009877","count":4},{"id":"GO:0046618","count":3},{"id":"GO:0006727","count":3},{"id":"GO:0010345","count":3},{"id":"GO:0006289","count":3}]},{"hash":"773965570716254778","title":"Macrophage NF-kappaB\u2013mediated inflammation","description":"The top terms cluster around macrophage differentiation regulation, macrophage inflammatory protein production, and NF-kappaB activity regulation, indicating a theme of macrophage-associated inflammatory signaling and NF-kappaB control. Some terms about skin/heart development may be incidental noise, but the core connection is immune/inflammatory regulation via NF-kappaB.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010745","count":4},{"id":"GO:0043588","count":3},{"id":"GO:0086070","count":3},{"id":"GO:1903444","count":3},{"id":"GO:0016477","count":3}]},{"hash":"42742963172401473","title":"Macrophage Inflammatory Signaling and Chemokine Production","description":"The top terms cluster around macrophage-related inflammatory regulation, including negative regulation of macrophage foam cell differentiation, NF-kappaB signaling regulation, and chemokine production (e.g., MIP-1 alpha and CCL5). These points indicate a cohesive theme of immune activation and inflammatory signaling, with supporting terms like cell migration and protein localization relevant to inflammatory responses; some terms appear ancillary (e.g., cardiac conduction), but the predominant pattern is macrophage-driven inflammation and chemokine regulation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010745","count":3},{"id":"GO:0086070","count":2},{"id":"GO:1903444","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0007253","count":2}]},{"hash":"176088015818640018","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018401","count":1},{"id":"GO:0055114","count":1},{"id":"GO:1901874","count":1},{"id":"GO:0032364","count":1},{"id":"GO:0009611","count":1}]},{"hash":"2292031413522350238","title":"Unknown","description":"Unknown","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902499","count":2},{"id":"GO:0070911","count":2},{"id":"GO:0010216","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0010332","count":2}]},{"hash":"903418149583287887","title":"Unknown","description":"These terms touch on cardiac cell communication, adipose differentiation, cell migration, NF-kappaB regulation, membrane protein localization, chemokine production, mechanosensory pain detection, and hepatocyte apoptosis. The set is highly heterogeneous with no single dominant biological theme, and there are no observed interactions among the proteins, making it difficult to assign a concise, representative label.","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086070","count":3},{"id":"GO:1903444","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0007253","count":3},{"id":"GO:0072660","count":3}]},{"hash":"822474125887008254","title":"Unknown","description":"The top GO terms span immune signaling (NF-kappaB regulation, NOD2 signaling), cardiac signaling (SA node action potential and cardiac cell communication), lipid metabolism (glycerophospholipid catabolic process), cytoplasmic NF-kappaB sequestration, and cell migration, with no clear shared function or pathway tying all proteins together. Edges are also zero, indicating no detected interactions to support a cohesive functional module. Therefore, there is no single representative theme to name the cluster. ","confidence":"","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":4},{"id":"GO:0098907","count":4},{"id":"GO:0007205","count":4},{"id":"GO:0046475","count":4},{"id":"GO:0070431","count":4}]},{"hash":"1980780980708318658","title":"Muscle Development and Contraction","description":"The Top Terms show a clear emphasis on muscle biology, including cardiac muscle development, skeletal muscle contraction regulation via calcium release, and muscle attachment, suggesting a cohesive theme around muscle structure and function. Some terms (RNA decay, spindle localization, nerve development) are less related, but they do not outweigh the dominant muscle-related signals. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000288","count":2},{"id":"GO:1902405","count":1},{"id":"GO:1902896","count":1},{"id":"GO:0016203","count":1},{"id":"GO:2001137","count":1}]},{"hash":"1270190399869525554","title":"Centromere Assembly and Mitotic Chromosome Segregation","description":"Dominant signals are centromere-associated chromatin assembly (CENP-A), mitotic cell cycle, and sister chromatid cohesion/segregation, pointing to roles in chromosome organization during mitosis. Other terms (e.g., ER-to-Golgi transport, obsolete histone deacetylation) seem less connected and may reflect annotation noise. Therefore, Centromere Assembly and Mitotic Chromosome Segregation fits best.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006888","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0061641","count":2},{"id":"GO:0051260","count":2}]},{"hash":"2225270498656522283","title":"Calcium signaling and excitability","description":"The top GO terms cluster around calcium ion transport and membrane depolarization, including high voltage-gated calcium channel transport, regulation of calcium transport, and Purkinje cell action potential depolarization. This points to a coherent theme of Ca2+-mediated signaling and electrical activity across tissues (cardiac, secretory, sensory), with some terms touching on calcium-dependent secretion and inflammatory mediator production as downstream effects. Overall, the cluster seems best described as calcium signaling and excitability.","confidence":"Medium","size":14,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903444","count":2},{"id":"GO:0061577","count":2},{"id":"GO:0060453","count":2},{"id":"GO:0051928","count":2},{"id":"GO:0086047","count":2}]},{"hash":"1995144566175791898","title":"Bacterial cell wall biosynthesis and antibiotic response","description":"The top GO terms point to teichoic acid biosynthesis, UDP-glucose metabolism, and cell wall organization, all characteristic of bacterial cell wall construction in Gram-positive organisms, with an accompanying response to antibiotics. Though a few terms are less coherent (e.g., mammalian developmental or signaling terms), the dominant signal reflects cell wall biosynthetic pathways and xenobiotic/antibiotic response, justifying this label.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071320","count":2},{"id":"GO:0048566","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0019350","count":2}]},{"hash":"1414720600106680600","title":"Neurodevelopmental transcription and signaling","description":"The dominant terms point to nervous system development (spinal cord, brain) and general multicellular development, paired with DNA-templated transcription and signaling pathways (TORC1, NOD2) and NF-kappaB regulation. This suggests a cluster of proteins involved in developmental transcriptional control and related signaling, with some immune signaling links.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":3},{"id":"GO:0032088","count":3},{"id":"GO:0070431","count":3},{"id":"GO:0007275","count":2},{"id":"GO:0006351","count":2}]},{"hash":"226016377819053265","title":"Phosphorylation Signaling Regulators","description":"These proteins appear to modulate phosphorylation-based signaling, given terms like positive regulation of protein serine/threonine kinase activity, positive regulation of protein autophosphorylation, and regulation of canonical NF-kappaB signaling. Additional terms touch on broader regulatory roles (hypoxia response, mRNA transport) and neuronal contexts (memory, retina layer formation), suggesting a general theme of signaling regulation with neural or cellular stress contexts. The lack of edges does not undermine a cohesive functional theme; the cluster likely comprises regulators that influence phosphorylation-driven pathways. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032516","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0051028","count":2},{"id":"GO:0010842","count":2}]},{"hash":"1329571429283278098","title":"RNA Processing and Cell Fate","description":"Based on the GO terms, the cluster centers on RNA metabolism and processing (rRNA maturation, mRNA processing, poly(A) tail shortening) and translation regulation via tRNA modification, with additional signals toward cellular stress and programmed cell death, suggesting a link to gene expression control and cell fate under stress.","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":1},{"id":"GO:0045347","count":1},{"id":"GO:0044829","count":1},{"id":"GO:0000289","count":1},{"id":"GO:1990983","count":1}]},{"hash":"298080462119853391","title":"TLR/NLRP3-driven innate immune activation","description":"The proteins are centered on innate immune sensing and response, with enrichment for TLR9 signaling, NLRP3 inflammasome assembly, interferon-beta production, dendritic cell cytokine regulation, and xenophagy, suggesting coordinated pathogen recognition and antigen presentation.","confidence":"High","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0045359","count":8},{"id":"GO:0034162","count":8},{"id":"GO:0044546","count":8},{"id":"GO:0031146","count":8},{"id":"GO:0046827","count":8}]},{"hash":"2284487797260823893","title":"Wnt-driven actin dynamics and cell migration","description":"This cluster combines several GO terms centered on Wnt signaling and cytoskeleton regulation (e.g., Wnt pathway, actin nucleation, vesicle transport along actin) with terms related to cell movement and adhesion (cell migration regulation, tight junction assembly, membrane rafts) and tissue remodeling (elastic fiber assembly, glomerulus development). The pattern suggests a cohesive theme of signaling interfacing with cytoskeletal dynamics and cell adhesion during development and remodeling. ","confidence":"Medium","size":14,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":2},{"id":"GO:0044855","count":1},{"id":"GO:0044655","count":1},{"id":"GO:0032835","count":1},{"id":"GO:0030050","count":1}]},{"hash":"494074851514990468","title":"Ubiquitination-Driven Protein Degradation","description":"The cluster's GO terms center on ubiquitination (K63-linked ubiquitination, autoubiquitination) and ubiquitin-dependent ERAD, plus chaperone-mediated assembly, pointing to protein quality control and proteasome-mediated turnover. Some peripheral terms appear incidental, but the dominant theme is ubiquitin-mediated degradation.","confidence":"High","size":13,"edges":32,"triangles":29,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0090035","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0071361","count":3}]},{"hash":"925799780271477040","title":"Ubiquitination and ERAD Proteostasis","description":"This cluster is enriched for ubiquitination- and ERAD-related processes (autoubiquitination, ubiquitin-dependent ERAD, and K63-linked ubiquitination) and regulation of chaperone-mediated proteasome assembly, pointing to involvement in tagging and degrading proteins via the ubiquitin\u2013proteasome system and ER-associated degradation. A few terms (ethanol/chitin responses, glucocorticoid metabolism) may reflect broader stress annotations but do not override the core ubiquitination/ERAD signal.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0090035","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0071361","count":3}]},{"hash":"946711890241212142","title":"Cytoskeleton dynamics in mitosis and intracellular transport","description":"These proteins cluster around microtubule- and cytoskeleton-related processes, including plus-end microtubule depolymerization, regulation of microtubule-based processes, and vesicle transport along microtubules, as well as mitotic events like chromosome recapture and contractile ring assembly. Chloroplast movement and integrin regulation further support MT-guided transport and cytokinesis contexts. Stress granule disassembly appears as a peripheral link to cytoskeletal remodeling under stress. Overall, the set is best described by cytoskeletal dynamics governing cell division and intracellular trafficking.","confidence":"Medium","size":13,"edges":77,"triangles":275,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0035617","count":7},{"id":"GO:0032487","count":6},{"id":"GO:0001560","count":6},{"id":"GO:0070462","count":6},{"id":"GO:0009904","count":6}]},{"hash":"839084267598105257","title":"Ubiquitin-Dependent Proteolysis & Circadian Regulation","description":"The top GO terms strongly point to ubiquitin-dependent protein catabolism, including SCF-dependent proteasomal degradation and ubiquitin signaling (K33-linked ubiquitination). The circadian rhythm regulation term supports clock-controlled protein turnover. Some development-related terms may reflect ubiquitin-mediated regulation in tissue formation. Overall, the cluster appears centered on ubiquitin-mediated proteolysis with a circadian regulation component.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":7},{"id":"GO:0042752","count":5},{"id":"GO:0031146","count":4},{"id":"GO:0000083","count":4},{"id":"GO:0030433","count":3}]},{"hash":"478794482647338527","title":"Ubiquitin-Mediated ERAD and Chaperone Regulation","description":"Most of the top GO terms cluster around ubiquitination and ER-associated degradation (ERAD), including ubiquitin-dependent pathways, K63-linked ubiquitination, and autoubiquitination, as well as chaperone-mediated protein complex assembly. This suggests a focus on protein quality control and degradation via ubiquitin signaling and ER-associated proteostasis. While a few terms reflect stress or hormone-related responses, the core theme is ubiquitin-driven proteostasis rather than a single signaling pathway.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:0090035","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0071361","count":3}]},{"hash":"929639490615701007","title":"Nicotinate/NAD metabolism and glycolysis","description":"The cluster\u2019s top GO terms are dominated by nicotinate nucleotide salvage and nicotinamide metabolic processes, along with glycolytic process, pointing to a shared role in NAD-related metabolism and energy production. Additional terms like uracil catabolic process, nitrogen utilization, and creatinine catabolic process suggest broader metabolic activity rather than a single, tight functional module. The absence of edges between members supports a heterogeneous set of metabolic proteins rather than a specific complex. Confidence: Medium","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019358","count":3},{"id":"GO:0006096","count":2},{"id":"GO:0006212","count":2},{"id":"GO:0002047","count":2},{"id":"GO:0001302","count":2}]},{"hash":"1181005349772420337","title":"NF-kB\u2013driven inflammatory signaling","description":"The cluster's top GO terms cluster around NF-kappaB regulation and inflammatory/immune responses (cytoplasmic sequestration of NF-kappaB and NF-kappaB transcription factor activity), plus macrophage/mast chemokine production and cell migration. An outlier term about hepatocyte apoptosis and another about pain perception can be linked to tissue stress and immune signaling, but the dominant pattern is NF-kB\u2013driven inflammatory signaling.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086070","count":9},{"id":"GO:1903444","count":9},{"id":"GO:0016477","count":9},{"id":"GO:0007253","count":9},{"id":"GO:0072660","count":9}]},{"hash":"707286283416521604","title":"Developmental Processes with Stress Responses","description":"Most terms cluster around developmental processes such as neural tube closure, forebrain and skeletal system development, and multicellular organism development, indicating a core developmental theme. The presence of stress-related terms (intrinsic apoptotic signaling in response to ER stress and cellular response to cadmium ion) and immune defense to Gram-positive bacteria adds a secondary layer of stress/defense signaling. Overall, the cluster appears to group proteins involved in development with accompanying stress-response pathways.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001843","count":12},{"id":"GO:0050830","count":12},{"id":"GO:0001403","count":12},{"id":"GO:0000278","count":12},{"id":"GO:0001501","count":12}]},{"hash":"1010110809474633187","title":"Steroid hormone metabolism and transcription regulation","description":"This cluster shows enrichment for androgen metabolic and catabolic processes and glucocorticoid biosynthesis, pointing to steroid hormone metabolism, with additional terms indicating transcriptional regulation (regulation of DNA-templated transcription). Some developmental terms (lung development, erythrocyte differentiation) are less central, likely representing broader roles or annotation noise; overall, the dominant signal is steroid metabolism with gene expression regulation.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042208","count":3},{"id":"GO:0045648","count":2},{"id":"GO:0051572","count":2},{"id":"GO:0008209","count":2}]},{"hash":"1936453310298079405","title":"RNA processing and transcription regulation","description":"This cluster shows a coherence around gene expression control, with terms like miRNA processing, maintenance of RNA location, negative regulation of transcription elongation, and other transcription-related processes. While a few terms appear organism-specific or unrelated (e.g., abscisic acid biosynthesis, cholangiocyte proliferation, mating-type regulation), the dominant theme is RNA processing and transcription regulation.","confidence":"Medium","size":13,"edges":12,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0033624","count":4},{"id":"GO:0009190","count":4},{"id":"GO:0009688","count":4},{"id":"GO:0090419","count":4},{"id":"GO:0051237","count":4}]},{"hash":"473822094046036441","title":"Diverse biosynthesis and antimicrobial response","description":"This cluster shows enrichment for multiple biosynthetic pathways (melanin, mycolic acid, glucocorticoid and androgen metabolism; acetoin catabolic) as well as antibiotic-related terms (response to antibiotic, antibiotic biosynthetic process). There is also a transcription regulation term and a developmental term (lung development), suggesting a broad mix of metabolic processes with antimicrobial context rather than a single cohesive function. Confidence: Medium","confidence":"","size":13,"edges":6,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0046677","count":8},{"id":"GO:0017000","count":8},{"id":"GO:0008209","count":7},{"id":"GO:0006355","count":7},{"id":"GO:0006710","count":7}]},{"hash":"985930594369573716","title":"RNA and Protein Methylation","description":"The top GO terms are dominated by methylation-related processes: rRNA methylation, peptidyl-lysine dimethylation/trimethylation, and N-terminal peptidyl-glycine methylation, with additional links to heterochromatin formation. This pattern points to a cluster centered on methyltransferase activities and related chromatin regulation, despite a few less-dominant metabolic terms. ","confidence":"High","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":4},{"id":"GO:0018027","count":3},{"id":"GO:0018023","count":3},{"id":"GO:0018013","count":3},{"id":"GO:0000183","count":3}]},{"hash":"1604756229462321897","title":"Lipid metabolism and sterol biosynthesis","description":"The cluster is dominated by lipid-related processes: unsaturated fatty acid biosynthetic, triglyceride biosynthetic, ergosterol biosynthetic regulation, and sphingolipid (mannosyl-inositol phosphorylceramide) metabolism, with supporting terms like sebaceous gland differentiation and myelin maintenance that relate to lipid-rich tissues. A few outliers (nitrate assimilation, gluconeogenesis, nitric oxide biosynthesis) may reflect broader metabolic roles or annotation noise, but the core signal points to lipid metabolism and sterol biosynthesis.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001949","count":2},{"id":"GO:0006675","count":2},{"id":"GO:0032443","count":2},{"id":"GO:0042128","count":2},{"id":"GO:0006636","count":2}]},{"hash":"2047065243886511466","title":"Translation and aminoacyl-tRNA charging","description":"This cluster is dominated by GO terms for aminoacyl-tRNA synthetases (Ile-, Met-, Val-, Leu-) and translation-related processes (translation, regulation of translational fidelity), indicating a core role in protein synthesis machinery. The presence of a few metabolism terms (pyruvate metabolism, gluconeogenesis) likely reflects broader cellular housekeeping links rather than a primary function, so the translation-centric label aptly captures the main theme.","confidence":"High","size":13,"edges":46,"triangles":68,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0000278","count":2},{"id":"GO:0006090","count":2},{"id":"GO:0006094","count":2},{"id":"GO:0006428","count":1},{"id":"GO:0006431","count":1}]},{"hash":"1034211512608914777","title":"Sterol and lipid biosynthesis","description":"The top GO terms cluster around sterol biosynthesis (ergosterol and cholesterol) and lipid metabolism (fatty acid and ether lipid pathways), with several annotations pointing to various steps in sterol and lipid biosynthesis. While some terms are broader (e.g., myelin maintenance, B cell chemotaxis), the dominant signal is lipid/sterol biosynthetic processes, suggesting a cohesive role in sterol and lipid metabolism across the proteins.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006696","count":3},{"id":"GO:0080064","count":3},{"id":"GO:0001949","count":3},{"id":"GO:0006675","count":3},{"id":"GO:0035754","count":3}]},{"hash":"598773945320557605","title":"Unknown","description":"The terms are highly heterogeneous, including thiamine and folate metabolism, lipopolysaccharide response, neurotransmitter catabolism/regulation (dopamine/serotonin), hematopoietic differentiation, and histone methylation regulation, with no clear unifying function across the cluster. This makes a cohesive, specific label unlikely.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0032496","count":5},{"id":"GO:0009228","count":3},{"id":"GO:0046653","count":3},{"id":"GO:0010725","count":3}]},{"hash":"559212600161030898","title":"Central carbon metabolism and quinone biosynthesis","description":"The cluster shows strong representation of core energy pathways (glycolysis, TCA cycle, beta-oxidation) and multiple catabolic processes, plus biosynthesis of quinones (phylloquinone and menaquinone). The presence of antibiotic biosynthetic potential also hints at broader secondary metabolism, but the dominant signal is central carbon metabolism coupled to quinone production.","confidence":"High","size":13,"edges":76,"triangles":265,"max_degree":12,"top_function":null,"top_go_terms":[{"id":"GO:0006635","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0010124","count":4},{"id":"GO:0042372","count":4},{"id":"GO:0006574","count":4}]},{"hash":"1441477691738289001","title":"Unknown","description":"The terms span mitotic cell cycle, multiple developmental processes (brain, lung), visual perception, B cell signaling, apoptotic and stress responses, and virus response, showing no single cohesive function for the cluster.","confidence":"","size":13,"edges":78,"triangles":286,"max_degree":12,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000278","count":12},{"id":"GO:0007601","count":12},{"id":"GO:0016477","count":9},{"id":"GO:0010898","count":9},{"id":"GO:0060484","count":9}]},{"hash":"2212176854147052598","title":"Capsule and Cell Wall Biosynthesis","description":"Likely represents a module of proteins involved in synthesis and organization of extracellular polysaccharides, including capsule polysaccharide biosynthesis and arabinan/ cell wall remodeling. The GO terms point to biosynthesis and structuring of the cell envelope, supported by notes on cell shape regulation and cell division. Some metabolism terms appear tangential to the core theme, possibly incidental annotations.","confidence":"Medium","size":13,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":2},{"id":"GO:0035884","count":1},{"id":"GO:0071555","count":1},{"id":"GO:0045227","count":1},{"id":"GO:0015945","count":1}]},{"hash":"42427819903986885","title":"Unknown","description":"The terms span immune signaling, ubiquitination, neuronal and muscular development, and cell division, with no single cohesive function or pathway linking the proteins; therefore no meaningful cluster label can be assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990390","count":1},{"id":"GO:0050853","count":1},{"id":"GO:1900242","count":1},{"id":"GO:0035853","count":1},{"id":"GO:0043380","count":1}]},{"hash":"619334759826368646","title":"Vacuolar amino acid transport","description":"The top GO terms point to transport of several amino acids (proline, asparagine, lysine, histidine, glutamate/glutamine) with multiple entries indicating transmembrane import into the vacuole. This pattern suggests a cohesive cluster of proteins involved in amino acid movement across membranes, especially into/out of vacuoles, rather than enzymes or signaling factors. Some terms are obsolete or ancillary (e.g., transcription regulation under pH), but the core theme remains amino acid transport and vacuolar trafficking.","confidence":"High","size":13,"edges":5,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1901481","count":1},{"id":"GO:0015824","count":1},{"id":"GO:0051365","count":1},{"id":"GO:0006867","count":1},{"id":"GO:0090517","count":1}]},{"hash":"987693800781790634","title":"Immune signaling and vascular remodeling","description":"The terms cluster around immune responses (defense against Gram-positive bacteria; IL-1\u03b2 and IL-8 production; NFAT signaling) and tissue remodeling processes (angiogenesis, elastin catabolic process, multicellular growth), suggesting a theme of inflammation-driven vascular remodeling and associated signaling, with some peripheral terms like synapse localization that may reflect broader signaling roles.","confidence":"Medium","size":13,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0050830","count":2},{"id":"GO:0071333","count":2},{"id":"GO:0045766","count":2},{"id":"GO:0014068","count":2},{"id":"GO:0051534","count":2}]},{"hash":"2155980947394792289","title":"Mitochondrial Transport and Membrane Potential Regulation","description":"The cluster is rich in terms tied to mitochondria: transport of ADP, ATP, alpha-ketoglutarate, and magnesium across the mitochondrial membrane, and regulation of membrane permeability and potential, plus responses to insulin/IGF signaling and oxidative stress, suggesting a coherent focus on mitochondrial energy metabolism and membrane dynamics.","confidence":"High","size":13,"edges":28,"triangles":28,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":5},{"id":"GO:0046902","count":4},{"id":"GO:0051881","count":4},{"id":"GO:0015742","count":4},{"id":"GO:1990314","count":4}]},{"hash":"1885405158630459595","title":"Cranial nerve morphogenesis and axon guidance","description":"The cluster is dominated by GO terms tied to cranial nerve development and guidance, including vagus nerve morphogenesis, facial nerve structural organization, glossopharyngeal nerve morphogenesis, and branchiomotor neuron axon guidance, suggesting a shared function in cranial nerve formation and pathfinding. Additional signaling-related terms (cell surface receptor tyrosine kinase signaling, regulation of GTPase activity) support a developmental signaling role, though a few terms like novobiocin biosynthetic process appear unrelated noise. Overall, the core theme matches cranial nerve morphogenesis and axon guidance.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0043642","count":1},{"id":"GO:0032259","count":1},{"id":"GO:0021644","count":1},{"id":"GO:0021612","count":1}]},{"hash":"1412061203611079698","title":"Epigenetic Regulation of Transcription","description":"These proteins appear linked to regulation of gene expression, with at least one term pointing to transcriptional activation by RNA polymerase II, and multiple histone modification terms (epigenetic marks) although several terms are obsolete. The presence of diverse regulatory processes (development, immune switching, drug response) suggests a broad regulatory cluster, but the core signal centers on transcription control and chromatin state.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090309","count":1},{"id":"GO:0045605","count":1},{"id":"GO:0034772","count":1},{"id":"GO:0007507","count":1},{"id":"GO:0048298","count":1}]},{"hash":"2216208502714557827","title":"ER protein folding and quality control","description":"Enriched terms. ER protein folding (GO:0034975), unfolded protein response (GO:0006986), response to heat (GO:0009408), and nuclear quality control by the ubiquitin-proteasome system (GO:0071630) point to cellular proteostasis, especially ER-associated folding and degradation under stress.","confidence":"High","size":13,"edges":15,"triangles":11,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1900035","count":3},{"id":"GO:1901621","count":3},{"id":"GO:0034975","count":3}]},{"hash":"526261238708472593","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006334","count":2},{"id":"GO:0080182","count":2},{"id":"GO:0000398","count":1},{"id":"GO:0000480","count":1},{"id":"GO:0071166","count":1}]},{"hash":"1567682536279370843","title":"Nuclear Transport and Transcription Regulation","description":"The GO terms point strongly to nuclear processes: import of NLS-bearing proteins into the nucleus, regulation of protein export from the nucleus, and DNA-templated transcription with core promoter binding, suggesting a cluster centered on nuclear gene expression regulation and trafficking. Additional signals like Wnt pathway regulation, apoptosis, and cell migration likely reflect downstream regulatory roles related to transcriptional control and signaling, but the core theme remains nuclear transport and transcription regulation.","confidence":"High","size":13,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0090090","count":3},{"id":"GO:0043065","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0006607","count":3}]},{"hash":"1648622550730979364","title":"DNA Replication, Repair, and Apoptosis Control","description":"This cluster is characterized by strong enrichment for DNA-related processes (DNA replication, DNA repair, DNA-templated transcription) as well as apoptosis and tightly regulated cell proliferation, indicating a cohesive role in maintaining genomic integrity and controlling cell fate. Additional terms like Wnt signaling modulation and innate immune response suggest broader signaling connections, but the core theme centers on DNA maintenance and programmed cell death decisions.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0016477","count":6},{"id":"GO:0043065","count":6},{"id":"GO:0008285","count":6},{"id":"GO:0033160","count":6}]},{"hash":"1686152526819099988","title":"Angiogenesis and Immune Receptor Signaling","description":"The top GO terms cluster around angiogenesis, VEGF receptor signaling, endothelial cell migration, and receptor-mediated signaling pathways (including B and T cell receptor signaling and serine/threonine kinase signaling), indicating a shared theme of receptor-driven signal transduction in vascular and immune contexts. Some terms like corpus callosum development and kinetochore localization appear peripheral, but the dominant pattern is vascular- and immune-related signaling.","confidence":"Medium","size":13,"edges":6,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001525","count":10},{"id":"GO:0022038","count":9},{"id":"GO:0050853","count":9},{"id":"GO:0007178","count":9},{"id":"GO:0033138","count":9}]},{"hash":"2186496922305505276","title":"Unknown","description":"The GO terms are diverse and span development, cell cycle, DNA replication, ion transport, immune defense, and ER-stress\u2013related apoptosis, with no clear, single theme linking all proteins. This makes it unclear how to assign a cohesive functional label with confidence.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006813","count":3},{"id":"GO:0001843","count":2},{"id":"GO:0050830","count":2},{"id":"GO:0001403","count":2},{"id":"GO:0000278","count":2}]},{"hash":"1006743239345767633","title":"Teichoic acid and cell wall polysaccharide biosynthesis","description":"The top terms cluster around glycosylation and polysaccharide assembly for the bacterial cell envelope, including teichoic acid biosynthesis, hyaluronan and cellulose biosynthesis, UDP-glucose metabolism, and O-linked protein glycosylation pathways. This points to a cohesive role in building and modifying cell wall components and surface glycoconjugates, hence this label.","confidence":"High","size":13,"edges":5,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0036108","count":3},{"id":"GO:0030213","count":3},{"id":"GO:0071555","count":3},{"id":"GO:0030244","count":3},{"id":"GO:0006011","count":3}]},{"hash":"1697887449654858870","title":"Mitochondrial transport and energy regulation","description":"The terms cluster around mitochondrial processes: regulation of membrane permeability and potential, transport of ADP, ATP, and \u03b1-ketoglutarate, Mg2+ export, and cellular insulin/IGF signaling responses, plus a response to superoxide. This points to a coherent theme of mitochondrion-centered energy metabolism and metabolite exchange, with nutrient-signaling links.","confidence":"High","size":13,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070542","count":3},{"id":"GO:0046902","count":2},{"id":"GO:0051881","count":2},{"id":"GO:0015742","count":2},{"id":"GO:0032869","count":2}]},{"hash":"1930402823373868918","title":"Stress-Responsive Ribosome Biogenesis and Translation","description":"This cluster centers on ribosome biogenesis and cytoplasmic translation (and ribosomal export), with accompanying abiotic stress responses (heat, desiccation) and osmoprotectant-related metabolism (trehalose, glucosylglycerol). The common thread is ribosome/translation activity modulated under stress, making this a concise label for the group.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0070415","count":3},{"id":"GO:0016311","count":3},{"id":"GO:0051473","count":3},{"id":"GO:0034605","count":3}]},{"hash":"457978099705533888","title":"Unknown","description":"The top terms span antibiotic biosynthesis, lipid metabolism, endocannabinoid signaling regulation, plant hormone biosynthesis, and plant development, with some terms marked obsolete; there is no clear shared function tying the proteins together, and the lack of edges suggests a diverse or noisy cluster. Therefore no specific, representative label can be assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":8},{"id":"GO:0019433","count":8},{"id":"GO:2000124","count":8},{"id":"GO:0055114","count":8},{"id":"GO:0046839","count":7}]},{"hash":"1815068383686221958","title":"RNA processing and translation components","description":"This cluster is dominated by terms tied to RNA metabolism: mRNA splicing via the spliceosome and spliceosomal conformational changes, rRNA base methylation, phenylalanyl-tRNA aminoacylation, and histidyl modification to diphthamide\u2014together pointing to RNA processing and translation-related functions (spliceosome activity, ribosome maturation, tRNA charging, and translation factor modifications). A few terms (e.g., cell cycle regulation, proteasome storage granule assembly) may reflect broader housekeeping roles or annotation noise. The lack of edges suggests these proteins are associated with related RNA/translation pathways rather than a single defined complex.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:0000393","count":2},{"id":"GO:0006432","count":1},{"id":"GO:1903955","count":1},{"id":"GO:0017183","count":1}]},{"hash":"1500063462738769613","title":"Ubiquitin-Proteasome and NF-\u03baB/ER Stress Signaling","description":"The terms cluster around protein ubiquitination and proteasomal degradation (SCF-dependent, ERAD), as well as NF-\u03baB regulatory pathways and ER-stress\u2013induced apoptotic signaling. Although a few outliers/obsolete terms and some non-proteostasis annotations appear, the core theme ties to proteostasis and stress-response signaling via ubiquitin pathways and NF-\u03baB.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0070059","count":2},{"id":"GO:0030433","count":2}]},{"hash":"630272035710475588","title":"Vacuolar V-ATPase assembly and acidification","description":"The GO terms converge on vacuolar function, especially proton-transporting V-type ATPase complex assembly, vacuolar acidification, and proton translocation, along with protein turnover in the vacuole and related excretion processes. While a couple of terms reflect broader or obsolete annotations (polyphosphate metabolism, Ehrlich pathway), the dominant signal points to a cluster of proteins involved in vacuolar proton pumping and acidification via the V-ATPase, i.e., vacuolar transport and pH regulation.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007035","count":1},{"id":"GO:0007039","count":1},{"id":"GO:0007588","count":1},{"id":"GO:0043181","count":1},{"id":"GO:0015986","count":1}]},{"hash":"718482336540531124","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010587","count":2},{"id":"GO:0033621","count":1},{"id":"GO:0048366","count":1},{"id":"GO:0048451","count":1},{"id":"GO:0006378","count":1}]},{"hash":"1863505643625191376","title":"Unknown","description":"Unknown","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000447","count":1},{"id":"GO:0048542","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0000461","count":1},{"id":"GO:0042274","count":1}]},{"hash":"1822252524027583625","title":"Unknown","description":"The top terms span diverse processes including several catabolic pathways (xylan, glucuronoside, lactose), neurotransmitter transport, protein ubiquitination and oligomerization, plus photosynthesis-related processes (xanthophyll cycle, chlorophyll metabolism) and heat response. This broad mix suggests no single cohesive function defining the cluster, despite a few photosynthesis-related terms, so a unified label cannot be confidently assigned.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045493","count":2},{"id":"GO:0006836","count":2},{"id":"GO:0051260","count":2},{"id":"GO:2000372","count":2},{"id":"GO:0016567","count":2}]},{"hash":"496957297847483752","title":"Unknown","description":"The top GO terms span mitochondrial RNA processing and translation, chloroplast RNA processing, and several animal development/regulatory terms (heart morphogenesis, left/right asymmetry, organ identity) with GPCR signaling regulation and cell cycle control. This combination points to multiple, disparate biological processes across organelles and development, lacking a single cohesive theme; plus the cluster shows no edges, suggesting it is not a unified functional module.","confidence":"","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070129","count":2},{"id":"GO:0090615","count":2},{"id":"GO:0055010","count":2},{"id":"GO:0031425","count":2},{"id":"GO:0071908","count":2}]},{"hash":"1536835062223014075","title":"Ceramide and glycosphingolipid transport","description":"Top GO terms are dominated by lipid transport and ceramide/glycosphingolipid metabolism (ceramide transport, ER-to-Golgi ceramide transport, glycolipid and glycosphingolipid transport). Some defense-related terms (defense response to bacterium, defense response to fungus, salicylic acid response) may reflect lipid-signaling roles in plant immunity, but the primary signal across terms is ceramide/glycosphingolipid transport and metabolism, suggesting a transport-focused lipid module.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0072488","count":1},{"id":"GO:0009751","count":1},{"id":"GO:1902389","count":1},{"id":"GO:0009816","count":1},{"id":"GO:0015695","count":1}]},{"hash":"401969138937273166","title":"RNA Processing and Decay Machinery","description":"The top GO terms cluster around nuclear RNA metabolism and RNA turnover, including nuclear polyadenylation-dependent rRNA decay, histone mRNA decay, snoRNA processing, nonfunctional rRNA decay, miRNA decay, and nuclear mRNA surveillance, plus transcription termination coupling. This points to a cohesive theme of RNA maturation, quality control, and decay in the nucleus, rather than a single protein complex. A mitotic cell cycle term appears incidental to this broader RNA-regulatory context.","confidence":"High","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071035","count":2},{"id":"GO:0071044","count":2},{"id":"GO:0030846","count":1},{"id":"GO:0043144","count":1},{"id":"GO:0070651","count":1}]},{"hash":"2059035451821061085","title":"Developmental processes","description":"The top GO terms cluster around developmental biology, including somitogenesis, axial and paraxial mesoderm development, and circulatory system development, with a separate term for rhabdomere development. This suggests a shared role in embryo development across tissues, though several metabolic annotations (cobalamin biosynthesis, glycolipid metabolism, capsule biosynthesis) and an obsolete glycosylation term hint at annotation noise or multi-function proteins. Overall, the cluster best represents developmental processes rather than a single, narrow function.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0042052","count":1},{"id":"GO:0045227","count":1},{"id":"GO:0072358","count":1},{"id":"GO:0033577","count":1}]},{"hash":"1731748637901425674","title":"Embryonic Axis Formation and Heart Development","description":"This cluster\u2019s top terms cluster around vertebrate development and body axis patterning, especially left-right symmetry determination, heart looping, and aorta development, along with spinal cord dorsal/ventral patterning. Some terms like maltose-related detection/transport and thermoception appear as outliers, but the dominant theme is embryonic axis formation and cardiovascular patterning.","confidence":"Medium","size":13,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007368","count":2},{"id":"GO:0042994","count":1},{"id":"GO:0034289","count":1},{"id":"GO:0001947","count":1},{"id":"GO:0035904","count":1}]},{"hash":"1920063500569701761","title":"Unknown","description":"The top terms show a mix of redox-related processes, regulation of cell cycle and mitochondrial function, vesicle acidification, growth, and several hormone- and development-related terms (cytokinin response, light signaling, endothelial morphogenesis). There is no clear unifying function across the cluster, so a single, intuitive label cannot be confidently assigned.","confidence":"","size":12,"edges":11,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0070527","count":2},{"id":"GO:0051726","count":2},{"id":"GO:0007035","count":2},{"id":"GO:0051881","count":2}]},{"hash":"1961927416933381087","title":"Ubiquitin-Dependent Proteostasis","description":"The top GO terms are dominated by ubiquitination-related processes: protein autoubiquitination, ubiquitin-dependent ERAD pathways, and K63-linked ubiquitination, all central to tagging proteins for degradation and quality control. Additional terms touch on protein complex assembly and stress-related responses, which can be downstream consequences of proteostasis regulation. Together, these indicate a coherent cluster centered on ubiquitin-mediated protein homeostasis and degradation pathways. Confidence: High","confidence":"","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":8},{"id":"GO:0030433","count":8},{"id":"GO:0070534","count":7},{"id":"GO:0030579","count":6},{"id":"GO:0090359","count":6}]},{"hash":"471394284078807952","title":"Steroid hormone and prostaglandin metabolism","description":"The top GO terms emphasize steroid biosynthesis (C21-steroid hormone biosynthetic process, androgen and progesterone metabolism) and prostaglandin signaling (cellular response to prostaglandin D stimulus), with related lipid pathways (bile acid biosynthetic process). This points to a cohesive theme around lipid-derived hormone production and eicosanoid signaling, justifying the label even with a few auxiliary terms.","confidence":"High","size":12,"edges":59,"triangles":156,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0071799","count":9},{"id":"GO:0001894","count":9},{"id":"GO:0006699","count":9},{"id":"GO:0018931","count":9},{"id":"GO:1901653","count":9}]},{"hash":"160524048366448512","title":"Actin Cytoskeleton Remodeling","description":"The cluster is dominated by GO terms tied to actin dynamics and cytoskeletal organization, including Arp2/3-mediated actin nucleation, sarcomere organization, and postsynaptic actin cytoskeleton organization. Additional terms like platelet aggregation and mitotic cytokinesis point to actin-driven remodeling across diverse contexts (platelets, muscle, neurons, cell division), suggesting a core theme of actin cytoskeleton remodeling in multiple cellular processes.","confidence":"High","size":12,"edges":35,"triangles":40,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0070527","count":5},{"id":"GO:0016344","count":5},{"id":"GO:0042766","count":5},{"id":"GO:0000281","count":5},{"id":"GO:0034314","count":5}]},{"hash":"839110984082015387","title":"Mitotic spindle assembly and microtubule regulation","description":"The cluster is dominated by GO terms tied to microtubule dynamics and mitosis\u2014plus-end depolymerization, regulation of microtubule-based processes, spindle midzone assembly, and mitotic chromosome handling\u2014along with actomyosin ring assembly and vesicle transport along microtubules. This cohesive set points to cytoskeletal regulation during cell division and associated intracellular transport, with signaling terms (e.g., Rap signaling) likely modulating these processes.","confidence":"High","size":12,"edges":63,"triangles":193,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0032487","count":12},{"id":"GO:0001560","count":12},{"id":"GO:0070462","count":12},{"id":"GO:0009904","count":12},{"id":"GO:1990942","count":12}]},{"hash":"262851718683837334","title":"Neural Development and Cell Cycle Regulation","description":"The top GO terms show a clear emphasis on neural biosignatures (forebrain development, neural tube closure) alongside cell division and transcription (mitotic spindle orientation, mitotic cell cycle, DNA-templated transcription). This suggests a cluster centered on neurodevelopmental processes paired with cell-cycle/ transcriptional regulation. Some stress response terms appear but are less representative of the main theme.","confidence":"Medium","size":12,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000132","count":3},{"id":"GO:0030900","count":3},{"id":"GO:0001843","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0071276","count":3}]},{"hash":"127752527153207001","title":"Ubiquitin-Dependent ERAD Proteostasis","description":"The top GO terms cluster around ubiquitination processes (protein autoubiquitination, K63-linked ubiquitination) and ubiquitin-dependent ERAD pathways, pointing to a group of proteins involved in tagging substrates for degradation and maintaining protein quality in the endoplasmic reticulum. The enrichment of chaperone-mediated assembly regulation supports a proteostasis theme, while other terms (ethanol response, chitin, glucocorticoid metabolism) appear as peripheral stress-related associations. Overall, this cluster most plausibly represents components of the ubiquitin-proteasome system and ERAD machinery governing protein homeostasis.","confidence":"High","size":12,"edges":11,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":12},{"id":"GO:0030433","count":12},{"id":"GO:0070534","count":9},{"id":"GO:0090035","count":8},{"id":"GO:0071361","count":8}]},{"hash":"330312604997030397","title":"Inflammatory signaling and chemokine production","description":"Based on the prominence of GO terms describing chemokine production (CXCL5, MIP-1\u03b1/CCL3), macrophage inflammatory signaling, and NF-kB\u2013related regulation, the cluster seems centered on inflammatory gene expression and immune signaling, with supporting themes of cell migration and pain perception. Some terms (heart and brown fat-related) are less cohesive but do not dominate the set.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086070","count":3},{"id":"GO:1903444","count":3},{"id":"GO:0016477","count":3},{"id":"GO:0007253","count":3},{"id":"GO:0072660","count":3}]},{"hash":"1272346080365781149","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning plant hormone responses (gibberellin), development (trichome patterning), apoptosis, viral processes, transcription, DNA repair, and chromatin/telomere regulation, with only a single connection observed among proteins. This lack of a cohesive functional theme and the presence of obsolete terms suggest there is no clear,Single cluster function to name; thus, Unknown with no confidence. ","confidence":"","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"cell differentiation","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0006915","count":4},{"id":"GO:0009739","count":3},{"id":"GO:1900033","count":3},{"id":"GO:1990414","count":3}]},{"hash":"7840104194134021","title":"Dendrite development and synaptic plasticity regulators","description":"The top GO terms point to neuronal morphogenesis and synaptic remodeling (positive regulation of synapse plasticity, dendrite development) with supporting roles in cytoskeletal signaling (Rho) and cellular polarization/localization (Golgi, centrosome, polarity). While some terms relate to general cell polarity (tight junctions, epithelial polarity), the combination is most consistent with a cluster of proteins regulating neuronal development and synaptic plasticity, with accompanying cytoskeletal and trafficking control.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051835","count":3},{"id":"GO:0035023","count":3},{"id":"GO:0070830","count":3},{"id":"GO:0035690","count":2},{"id":"GO:0016358","count":2}]},{"hash":"340215905915081050","title":"Cell Cycle Checkpoint and Stress Signaling Regulators","description":"The top GO terms point to mitotic spindle assembly checkpoint signaling (cell cycle control), regulation of JNK stress signaling, and redox detoxification, suggesting a group of proteins coordinating cellular stress responses with cell-cycle/checkpoint regulation and fate decisions. Some terms are broader (viral process, vitamin D response), but the strongest signals support a cohesive theme around stress and checkpoint signaling.","confidence":"Medium","size":12,"edges":9,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0070535","count":2},{"id":"GO:0044810","count":2},{"id":"GO:0046328","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0098869","count":2}]},{"hash":"2217393624939490916","title":"DNA replication and cell cycle regulation","description":"This cluster is dominated by GO terms tied to nuclear DNA replication, centrosome cycle, and positive regulation of the nuclear cell cycle DNA replication, suggesting a core role in DNA synthesis and cell-cycle progression. Additional terms related to telomere maintenance and chromatin dynamics (histone acetylation, nucleosome positioning, transcription start site regulation) indicate coordinated chromatin regulation during replication and division, with one outlier development term. Overall, the theme points to nuclear DNA replication and cell-cycle control with accompanying chromatin remodeling.","confidence":"High","size":12,"edges":40,"triangles":53,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0007098","count":11},{"id":"GO:0006260","count":11},{"id":"GO:0010571","count":11},{"id":"GO:0048701","count":11},{"id":"GO:0071441","count":6}]},{"hash":"321134246924788274","title":"Mesodermal development and vasculogenesis","description":"The cluster is dominated by GO terms tied to mesoderm-derived tissue development and vascular formation, including erythrocyte development, mesodermal differentiation, and positive regulation of vasculogenesis, with a note of Notch pathway regulation. Some terms appear obsolete or unrelated (e.g., histidine/LPS biosynthesis) and may reflect annotation noise, but the core signal points to mesodermal development and angiogenesis.","confidence":"High","size":12,"edges":36,"triangles":47,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0009103","count":2},{"id":"GO:0016311","count":2},{"id":"GO:0000105","count":2},{"id":"GO:0048821","count":2}]},{"hash":"1121017136937851866","title":"DNA Repair and SOS Response","description":"Most frequent GO terms center on DNA repair (nucleotide-excision repair), the SOS response, and DNA replication, suggesting the cluster is focused on genome maintenance and DNA damage signaling. Other terms like bacteriocin transport, teichoic acid transport, xenobiotic export, and embryonic cranial skeleton morphogenesis likely reflect annotation cross-terms or distant homology rather than core functions; the dominant DNA metabolism theme justifies labeling as DNA Repair and SOS Response.","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006289","count":4},{"id":"GO:0009432","count":4},{"id":"GO:0006260","count":3},{"id":"GO:0048701","count":3},{"id":"GO:0071361","count":2}]},{"hash":"1433010339163653891","title":"Redox Homeostasis and Oxidative Stress Response","description":"This cluster is dominated by GO terms related to managing oxidative stress and redox balance: cellular response to oxidative stress, cellular oxidant detoxification, and cell redox homeostasis, plus protein deglutathionylation. While a couple terms are obsolete or less central (and one transcription regulation term appears), the consistent redox/oxidative stress theme makes this label representative of the proteins\u2019 function.","confidence":"High","size":12,"edges":10,"triangles":0,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0034599","count":3},{"id":"GO:0098869","count":3},{"id":"GO:1903026","count":3},{"id":"GO:0045454","count":3}]},{"hash":"2090979104705146797","title":"Neuronal excitability and synaptic regulation","description":"The top GO terms cluster around neural signaling and membrane excitability: membrane hyperpolarization, regulation of potassium channels, nociception, and long-term synaptic depression, with circadian rhythm effects and some cytoskeletal remodeling (stress fiber assembly) also aligning with neuronal processes. A couple terms (e.g., sperm-egg binding) appear incidental, but the overall pattern points to neuronal signaling and plasticity. Confidence: Medium.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007339","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0051260","count":1},{"id":"GO:1900454","count":1},{"id":"GO:0071286","count":1}]},{"hash":"468352804267929861","title":"Negative regulation of innate inflammatory signaling","description":"Most top terms point to dampening of inflammatory pathways (interferon-beta, TNF, IL-1, IL-8, TLR signaling, NF-kappaB). This suggests the cluster comprises regulators that restrain innate immune responses. A couple of terms (mRNA splicing, embryonic axis) are unrelated to immunity and may reflect annotation noise, but the core theme remains inhibitory immune signaling.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032688","count":1},{"id":"GO:0071356","count":1},{"id":"GO:0034122","count":1},{"id":"GO:0071347","count":1},{"id":"GO:0032717","count":1}]},{"hash":"415687257348754794","title":"Chromatin Regulation and Transcription Elongation","description":"The dominant GO terms are about transcription elongation by RNA polymerase II and its regulation, plus chromatin-related processes such as histone H2B ubiquitination and heterochromatin boundary formation, which collectively point to transcriptional control coupled with chromatin state. A few terms touch development and cell fate, which can be tied to transcriptional regulation during development, but the core theme remains transcription elongation and chromatin dynamics.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032968","count":2},{"id":"GO:0006368","count":2},{"id":"GO:0019827","count":1},{"id":"GO:0010048","count":1},{"id":"GO:0035206","count":1}]},{"hash":"1654032994710341793","title":"DNA replication and repair machinery","description":"The cluster is dominated by GO terms for DNA replication and DNA damage response (DNA replication, mitotic DNA replication checkpoint signaling, UV-damage excision repair, and translesion synthesis). Other terms emphasize protein oligomerization/complex assembly, which is common for replication/repair complexes. Some annotations about peroxisome import and mitochondrial complex III assembly may reflect multifunctional proteins rather than a single organelle-specific function. Overall, the strongest shared theme is genome maintenance through replication and repair.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051260","count":4},{"id":"GO:0016562","count":4},{"id":"GO:0006260","count":4},{"id":"GO:0034214","count":4},{"id":"GO:0034551","count":4}]},{"hash":"881869780093339701","title":"Actin polymerization and lamellipodium assembly","description":"This cluster is dominated by GO terms related to actin dynamics: actin nucleation, filament polymerization, filament bundle assembly, and barbed-end capping, as well as lamellipodium morphogenesis, all pointing to actin cytoskeleton remodeling and protrusive structure formation. The COPII vesicle cargo loading term can be tied to actin-mediated trafficking. Although there are a couple of outliers (amyloid fibril formation, spliceosome change), the core pattern supports actin-driven cytoskeleton remodeling and lamellipodium formation.","confidence":"High","size":12,"edges":7,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0051127","count":2},{"id":"GO:0090110","count":2},{"id":"GO:1990000","count":2},{"id":"GO:0051017","count":2},{"id":"GO:0051016","count":2}]},{"hash":"2054811953225541910","title":"Pole plasm and oskar mRNA localization","description":"The cluster is dominated by GO terms tied to oocyte polarity, pole plasm, and oskar mRNA localization (e.g., oocyte microtubule cytoskeleton polarization, pole plasm oskar mRNA localization, pole plasm protein localization, mRNA processing). This points to a shared function in assembling and localizing pole plasm components and associated mRNA within the oocyte. Some other terms (glycogen metabolism, enterobacterial antigen biosynthesis) seem unrelated and may reflect annotation noise.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009966","count":1},{"id":"GO:0043666","count":1},{"id":"GO:0043086","count":1},{"id":"GO:0005977","count":1},{"id":"GO:0008103","count":1}]},{"hash":"1562484368682354733","title":"ER Protein Folding and Heat Stress Regulation","description":"This cluster is dominated by GO terms related to protein folding in the endoplasmic reticulum, unfolded protein response, and heat stress response. The terms protein folding in ER, response to unfolded protein, response to heat, and negative regulation of cellular response to heat point to a shared function in maintaining protein quality under stress (ER stress/UPR). The presence of negative regulation of protein kinase activity aligns with regulatory adjustments during stress. Some terms like DNA replication and translational frameshifting are less directly connected, possibly reflecting broader cellular processes or annotation noise, but the core theme remains ER-associated quality control.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0009408","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1900035","count":3},{"id":"GO:1901621","count":3}]},{"hash":"517240569748279746","title":"Unknown","description":"The Top Terms are highly diverse (insulin secretion, activin signaling, redox response, cardiac morphogenesis, neural activity, hydrogen peroxide response, cell division, among others) and there is no single coherent functional theme linking them. Additionally, the cluster has no edges or interactions, suggesting the proteins do not share a common pathway or process. Therefore a clear, specific functional label cannot be assigned beyond Unknown.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030073","count":1},{"id":"GO:0032925","count":1},{"id":"GO:1901710","count":1},{"id":"GO:0055010","count":1},{"id":"GO:0051775","count":1}]},{"hash":"1842253948030873746","title":"Heat Stress Proteostasis","description":"The cluster is dominated by GO terms related to heat response, unfolded protein response, ER protein folding, and nuclear proteasome-mediated quality control, pointing to a cohesive role in maintaining protein homeostasis under thermal stress. Some terms like DNA replication or signaling regulation appear as secondary associations, but the core signal is proteostasis and chaperone/quality-control activity in response to heat.  ","confidence":"High","size":12,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1900035","count":3},{"id":"GO:1901621","count":3},{"id":"GO:0034975","count":3}]},{"hash":"1741986551607991943","title":"Unknown","description":"The GO terms cover several distinct areas (protein modifications such as carbamoylation and ubiquitination, protein folding/stabilization, neural processes like synapse organization and neuron apoptosis, chromatin regulation, and signaling pathway modulation including Wnt and TGF-beta). There is no single coherent function that ties these proteins together, so I cannot assign a specific, representative name with confidence.","confidence":"","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046944","count":1},{"id":"GO:0050821","count":1},{"id":"GO:0050808","count":1},{"id":"GO:0061051","count":1},{"id":"GO:0090263","count":1}]},{"hash":"527251046011024620","title":"Dopaminergic Neuron Function and Mitochondrial Regulation","description":"These terms cluster around dopamine biology in neurons: dopamine metabolic process; dopaminergic synaptic transmission; dopaminergic neuron differentiation; neuron projection development. Additionally, several terms pertain to neuronal energy/mitochondrial function (regulation of mitochondrial membrane potential and permeability; alpha-ketoglutarate transport). The combination suggests a theme of dopaminergic neuron development and signaling with mitochondrial energy regulation.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":1},{"id":"GO:0070050","count":1},{"id":"GO:0042417","count":1},{"id":"GO:0002014","count":1},{"id":"GO:0001963","count":1}]},{"hash":"107943834227413287","title":"Unknown","description":"Top terms span diverse developmental and cellular processes with no single unifying function; developmental terms (somatic embryogenesis, microgametogenesis, atrioventricular canal development, cardiac jelly) coexist with basic cellular machinery (RNA Pol II preinitiation complex assembly, vesicle transport, protein secretion, phosphate transport), making a coherent cluster label unlikely.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":1},{"id":"GO:0010262","count":1},{"id":"GO:0055046","count":1},{"id":"GO:0045466","count":1},{"id":"GO:0036302","count":1}]},{"hash":"899582629831666065","title":"Ribosome Biogenesis and rRNA Maturation","description":"The top GO terms point to maturation of SSU/LSU rRNA, ribosome biogenesis, translation, and export of the large subunit, indicating a module of proteins involved in ribosome assembly. The inclusion of spliceosome-related RNA processing terms suggests a secondary association with RNA processing. Overall, this cluster appears to form a coherent ribosome biogenesis/RNA maturation program.","confidence":"High","size":12,"edges":25,"triangles":24,"max_degree":8,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0000462","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0042254","count":4},{"id":"GO:0006412","count":4},{"id":"GO:0000463","count":3}]},{"hash":"1075151466131353998","title":"Transport and stress-response proteins","description":"GO terms cluster around membrane and metabolite transport (glycine betaine transport, xenobiotic export, long-chain fatty acid import into peroxisome, teichoic acid transport) with supporting regulatory and maintenance processes (protein dephosphorylation, proteasome regulatory particle assembly, nucleotide-excision repair, cell division, photoinhibition). This suggests a heterogeneous cluster where transport is a core theme, linked to general stress response and protein/homeostatic regulation.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031460","count":3},{"id":"GO:0016055","count":3},{"id":"GO:0006470","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0070682","count":2}]},{"hash":"984345722531893825","title":"Immune Activation and Cell Migration","description":"The cluster shows strong representation of immune-related processes (defense response to Gram-positive bacteria, IL-4 production, B cell affinity maturation, GM-CSF response) alongside cell movement (cell migration) and PI3K/AKT signaling, suggesting a theme of immune activation with motility. Some terms on development and protein stability are present but do not outweigh the immune/migration signal. ","confidence":"Medium","size":12,"edges":16,"triangles":9,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016477","count":7},{"id":"GO:0050830","count":7},{"id":"GO:0060044","count":7},{"id":"GO:0032633","count":7},{"id":"GO:0043491","count":7}]},{"hash":"705126277173796348","title":"Sugar and metabolite transporters","description":"The Top Terms are dominated by membrane transport activities for a variety of substrates, including glucose (and D-glucose transmembrane transport), fructose, trehalose, urate, dehydroascorbic acid, selenite, and organic anions, as well as an osmotic stress response. This points to a cohesive role as membrane transporters handling sugars and other metabolites rather than a single substrate, despite the single-edge network. Confidence: High","confidence":"","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1904728","count":11},{"id":"GO:0044381","count":11},{"id":"GO:0015747","count":11},{"id":"GO:0070837","count":11},{"id":"GO:0015771","count":11}]},{"hash":"1881670659014816916","title":"Innate Immune Signaling and Inflammasome Activation","description":"This cluster centers on innate immune pathways, with GO terms for TLR9 signaling, NLRP3 inflammasome assembly, regulation of non-canonical NF-kappaB signaling, and IL-18 production, indicating involvement in inflammatory signaling and cytokine production. Additional terms like translation, rRNA base methylation, and SCF-mediated proteasomal degradation suggest general protein synthesis and turnover processes that support immune responses but are not the defining theme. Overall, the dominant signal is innate immune activation and cytokine production.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0055114","count":2},{"id":"GO:0030324","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0070475","count":2}]},{"hash":"62833250993091180","title":"Mitochondrial protein import and respiration","description":"This cluster is dominated by GO terms linked to mitochondria and energy production: protein insertion into the mitochondrial inner membrane, aerobic respiration, and proton transmembrane transport, indicating a focus on mitochondrial protein import and mitochondrial energy metabolism. Additional terms relate to protein turnover (ubiquitin recycling, protein catabolic process), suggesting coordinated protein quality control with mitochondrial function. Some terms about viral processes and symbiont entry appear as outliers but do not define the primary theme. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045039","count":2},{"id":"GO:0009060","count":2},{"id":"GO:0016032","count":2},{"id":"GO:1902600","count":2},{"id":"GO:0006627","count":2}]},{"hash":"2088841099710244698","title":"Plant Golgi sugar transport and glycosylation","description":"The cluster\u2019s top GO terms cluster around transmembrane transport of sugar phosphates and nucleotide-sugars into the Golgi lumen (UDP-glucose, GDP-fucose, phosphoglycerate, triose phosphate, phosphoenolpyruvate), and glycosylation processes (protein O-linked glycosylation via fucose, fucosylation). The presence of root hair and lateral root development terms suggests plant-specific roles in cell wall biosynthesis and morphogenesis, consistent with Golgi-based glycan assembly and sugar-nucleotide transport. Despite many obsolete terms, the core theme points to Golgi-associated glycosylation by import of sugar substrates in plants.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018298","count":2},{"id":"GO:0035436","count":1},{"id":"GO:0036071","count":1},{"id":"GO:0015713","count":1},{"id":"GO:0015786","count":1}]},{"hash":"71310227408238558","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0042619","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0034720","count":2},{"id":"GO:0006096","count":2}]},{"hash":"1916814391923932198","title":"Peroxisomal Fatty Acid Metabolism in Seeds","description":"The cluster's terms cluster fatty acid biosynthesis and metabolism (including very long-chain and medium-chain fatty acids) and peroxisomal matrix protein import, plus seed coat development, pointing to a seed-specific peroxisomal lipid-processing theme. While some terms are broader (e.g., cellular stress), the dominant pattern is peroxisomal fatty acid metabolism in seeds.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051301","count":5},{"id":"GO:0016558","count":4},{"id":"GO:0034599","count":4},{"id":"GO:0001579","count":4},{"id":"GO:0010124","count":4}]},{"hash":"2215221716343321071","title":"Unknown","description":"Unknown","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":3},{"id":"GO:0042351","count":3},{"id":"GO:0080110","count":3},{"id":"GO:0042619","count":3},{"id":"GO:0009244","count":3}]},{"hash":"752150918749017581","title":"Mitotic progression and cell cycle regulation","description":"Top GO terms cluster around mitosis and cell cycle control, including G1/S and G2/M transitions, spindle pole separation, and chromosome condensation (histone H3-S10 phosphorylation), suggesting a core function in mitotic progression. Some terms (e.g., response to cocaine, antibiotic biosynthetic process) appear less connected and may reflect broader annotations or noise, but the dominant signal is cell cycle regulation.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":4},{"id":"GO:0042220","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0010696","count":3},{"id":"GO:2000775","count":3}]},{"hash":"1094487789322097896","title":"Brush border microvilli regulation","description":"This cluster shows explicit enrichment for microvillus-related terms, including terminal web assembly and regulation of microvillus length, plus intestinal glucose absorption, all pointing to brush border structure and function in intestinal epithelial cells. The presence of trafficking-related terms (ER-Golgi transport, COPII coating) may reflect shared secretory pathway components, but the strongest signal is microvilli regulation, guiding a brush border-focused label.","confidence":"Medium","size":12,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1902896","count":2},{"id":"GO:0032532","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0001951","count":2}]},{"hash":"1597817381736691050","title":"Unknown","description":"The terms span metabolism (terpenoid/IPP; CoA biosynthesis), stress xenobiotic response, redox, signaling (salicylic acid pathway), and development (facioacoustic ganglion, angiogenesis). There is no single shared process tying them together, and the graph has no edges; thus no coherent cluster function can be asserted.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0002042","count":2},{"id":"GO:0042493","count":2},{"id":"GO:0016310","count":1},{"id":"GO:0015937","count":1}]},{"hash":"1228869495256784274","title":"Redox Metabolism and PPP/Glycerol Pathways","description":"This cluster centers on redox biology (oxidation-reduction, oxidant detoxification) and sugar metabolism (reductive pentose-phosphate cycle, xylulose biosynthesis, glycerol catabolism), suggesting enzymes that balance redox state while processing carbon via PPP and glycerol pathways. The presence of antibiotic response hints at stress regulation but the core signal is redox-linked sugar metabolism.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0051289","count":2},{"id":"GO:0019563","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0019253","count":1}]},{"hash":"766019373498518005","title":"Protein and rRNA methylation machinery","description":"This cluster is dominated by GO terms related to methylation: peptidyl-lysine dimethylation and trimethylation, N-terminal peptidyl-glycine methylation, and especially rRNA methylation, along with rDNA heterochromatin formation. Together these point to enzymes that catalyze methylation on proteins and RNA, often influencing chromatin state and ribosome biogenesis. Some other terms like insulin secretion or cardiac morphogenesis are less directly connected, but the methylation/chromatin theme is the strongest signal.","confidence":"High","size":12,"edges":63,"triangles":190,"max_degree":11,"top_function":null,"top_go_terms":[{"id":"GO:0000183","count":5},{"id":"GO:0018027","count":4},{"id":"GO:0018023","count":4},{"id":"GO:0031167","count":4},{"id":"GO:0018013","count":4}]},{"hash":"6414457810698418","title":"Ribosome Biogenesis and RNA Processing","description":"Top GO terms point to ribosomal large subunit biogenesis, rRNA maturation (both SSU and LSU), and mRNA splicing, suggesting a shared role in RNA processing and ribosome assembly. Some other terms (neural development, cadmium response) are likely annotations from broader functions and not central to this cluster, so the core signal is RNA maturation and ribosome biogenesis.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0007584","count":4},{"id":"GO:0030900","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0001843","count":4},{"id":"GO:0042273","count":4}]},{"hash":"2278869007058819929","title":"RNA Pol II transcription termination and CTD dephosphorylation","description":"This cluster is dominated by GO:0006369 (termination of RNA polymerase II transcription) and GO:0070940 (CTD dephosphorylation), indicating a core theme around transcription termination and CTD regulation.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":2},{"id":"GO:0070940","count":1},{"id":"GO:0010526","count":1},{"id":"GO:0006379","count":1},{"id":"GO:0006378","count":1}]},{"hash":"2011447492493026607","title":"Mitotic progression and transcription","description":"Top GO terms are dominated by mitosis-related processes (G1/S and G2/M transitions, spindle pole separation, re-entry into mitosis) and DNA-templated transcription, pointing to proteins involved in driving cell cycle progression and associated gene expression. Some peripheral terms (insulin signaling regulation, potassium transport) appear but do not define the main theme.","confidence":"High","size":12,"edges":13,"triangles":3,"max_degree":5,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0010696","count":3},{"id":"GO:2000775","count":3},{"id":"GO:0000082","count":3},{"id":"GO:0000086","count":3},{"id":"GO:0046626","count":3}]},{"hash":"2236226794126534122","title":"Unknown","description":"The terms span multiple distinct biological themes (mitotic spindle assembly, SA node regulation, GPCR signaling, cardiac cell communication, brown fat differentiation, cell migration, NF-kappaB sequestration, membrane protein localization, chemokine production, and mechanosensation). There is no single unifying function or pathway that ties these proteins together in this cluster, and the terms reflect diverse contexts rather than a cohesive biological role. ","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051225","count":3},{"id":"GO:0098907","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0086070","count":2},{"id":"GO:1903444","count":2}]},{"hash":"1158437538897316992","title":"Proteostasis and Signaling Regulation","description":"This cluster centers on ubiquitin-dependent protein catabolic process and proteasome assembly, indicating a core proteostasis function. It also features GO terms related to regulation of kinase activity and GTPase activity, pointing to modulation of signaling pathways. Despite some plant- or tissue-specific terms present (chlorophyll biosynthesis, stamen formation, SA node signaling, brown fat differentiation, cell migration), the convergent theme is controlled degradation and signaling regulation.","confidence":"Medium","size":12,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006511","count":4},{"id":"GO:0006469","count":3},{"id":"GO:0007205","count":3},{"id":"GO:0043248","count":3},{"id":"GO:0015995","count":3}]},{"hash":"1923774952995980896","title":"Nematode molting and metabolism","description":"The top terms include nematode-specific processes (molting cycle with cuticle components and pharyngeal pumping) alongside general metabolic processes (proteolysis, nicotinamide nucleotide metabolism, and mRNA decapping). This points to a cluster centered on nematode developmental physiology coupled with basic cellular metabolism, though the connections are broad rather than tightly unified. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018996","count":1},{"id":"GO:0043050","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0046496","count":1},{"id":"GO:0031087","count":1}]},{"hash":"1389536657378072721","title":"Melanin biosynthesis and melanosome organization","description":"The top GO terms are dominated by pigmentation and melanin-related processes (pigmentation, melanin biosynthetic process from tyrosine, and melanosome organization), indicating the cluster principally relates to melanin production and pigment-containing organelle organization. A few unrelated terms appear but are less representative of the overall function.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043473","count":2},{"id":"GO:0002052","count":2},{"id":"GO:0006583","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0021847","count":2}]},{"hash":"1160708416894746439","title":"RNA and protein methylation","description":"This cluster is driven by methylation chemistry. The top terms include several forms of methylation (peptidyl-lysine dimethylation/trimethylation, N-terminal methylation) and RNA methylation (rRNA methylation, 7-methylguanosine cap), plus mRNA capping. This suggests a group of methyltransferases involved in RNA modification and, broadly, protein methylation. Some additional terms reference related chromatin methylation and other metabolic processes, but the dominant signal is methyltransferase/RNA modification activity.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018027","count":3},{"id":"GO:0031167","count":3},{"id":"GO:0018023","count":3},{"id":"GO:0018013","count":3},{"id":"GO:0000183","count":3}]},{"hash":"2275273995892432712","title":"Nucleotide metabolism and RNA editing","description":"Top GO terms are largely about nucleotide metabolism and RNA processing: cytosine metabolic process, UMP salvage, uridine biosynthetic process, deoxycytidine catabolic process, and guanine catabolic process, plus tRNA wobble adenosine-to-inosine editing. A riboflavin biosynthesis term also appears, which relates to metabolic cofactors often tied to nucleotide metabolism. A couple of signaling terms (NOD2 signaling, NF-kappaB regulation) and antibiotic response are present but less representative, suggesting the core theme is nucleotide metabolism with a minor signaling noise.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":2},{"id":"GO:0070431","count":2},{"id":"GO:0019858","count":1},{"id":"GO:0044206","count":1},{"id":"GO:0002100","count":1}]},{"hash":"1278068177187339382","title":"Regulation of transcription, cell cycle, and apoptosis","description":"Top GO terms show negative regulation of transcription by RNA polymerase II, regulation of the cell cycle, and apoptotic/necroptotic pathways, with supporting signals for ubiquitination, spindle assembly, and development. Together these terms point to proteins that broadly regulate gene expression and cell fate decisions (proliferation, survival, and differentiation), rather than a single pathway.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":5},{"id":"GO:0071157","count":4},{"id":"GO:0034121","count":4},{"id":"GO:0043066","count":4},{"id":"GO:0000209","count":4}]},{"hash":"2019016043158028156","title":"Sterol and lipid biosynthesis","description":"The top GO terms are dominated by sterol and lipid metabolism (ergosterol biosynthesis, sterol oxidations, fatty acid and ether lipid metabolism, and cholesterol biosynthesis), indicating a cohesive function in lipid/sterol production. A few terms related to skin and immune contexts (sebaceous gland differentiation, B cell chemotaxis, myelin maintenance) may reflect broader lipid biology or annotation noise, but do not override the primary lipid biosynthesis theme.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006696","count":2},{"id":"GO:0080064","count":2},{"id":"GO:0001949","count":2},{"id":"GO:0006675","count":2},{"id":"GO:0035754","count":2}]},{"hash":"898907650490750352","title":"Unknown","description":"The Top Terms are highly diverse, spanning pain perception, histamine response, heparin and copper starvation responses, protoxylem development, and amino acid catabolism, with no clear common biological theme. The absence of edges between proteins further suggests a lack of cohesive functional linkage. Therefore, no single representative function emerges for this cluster.","confidence":"","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902283","count":2},{"id":"GO:0050966","count":2},{"id":"GO:0071504","count":1},{"id":"GO:0090059","count":1},{"id":"GO:0046677","count":1}]},{"hash":"446300086613304120","title":"IGF/EGF signaling and cell migration","description":"The cluster\u2019s top GO terms center on insulin-like growth factor receptor signaling and epidermal growth factor\u2013related responses, with downstream processes such as integrin activation and cell migration, and even heart development, suggesting a cohesive theme of growth factor signaling guiding cell movement and development. Some terms (e.g., protein tetramerization, salicylic acid response) are less directly related but do not override the main signal.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048009","count":2},{"id":"GO:0051262","count":2},{"id":"GO:0045725","count":2},{"id":"GO:0014065","count":2},{"id":"GO:0007205","count":2}]},{"hash":"535338445233463266","title":"Fructose and glycolysis metabolism","description":"This cluster is dominated by carbohydrate metabolism terms: fructose metabolic process, fructose 2,6-bisphosphate metabolism, carbohydrate phosphorylation, regulation of the pentose-phosphate shunt, and pathways related to glucose catabolism toward lactate. Thyroid hormone generation hints at hormonal metabolic regulation, supporting an energy/metabolism theme. A couple terms (retina development regulation, cobalt ion response) are outliers but do not obscure the main metabolic signal.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061074","count":1},{"id":"GO:0042446","count":1},{"id":"GO:0006590","count":1},{"id":"GO:0042404","count":1},{"id":"GO:0006000","count":1}]},{"hash":"339972208295998517","title":"tRNA wobble modification and nucleic acid repair","description":"This cluster centers on tRNA wobble uridine modification and regulation of translation via tRNA modification, with supporting signals from mRNA processing and RNA/DNA repair pathways; plus a stress-response angle suggested by mitochondrial permeability and programmed cell death terms. The core theme appears to be nucleic acid modification affecting translation and genome maintenance.","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1990983","count":2},{"id":"GO:1902445","count":2},{"id":"GO:0035553","count":2},{"id":"GO:0006281","count":2},{"id":"GO:0012501","count":2}]},{"hash":"2190032900113058506","title":"Metabolite Transporters","description":"This cluster is dominated by GO terms for transporting a range of metabolites (sugars like glucose and trehalose, arabinose, urate, nitrite/nitrate, dehydroascorbic acid) and related nutrient uptake processes, indicating these proteins likely function as diverse membrane transporters involved in nutrient acquisition and metabolic balance, even though no edges connect them in this instance.","confidence":"High","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042149","count":2},{"id":"GO:0015706","count":1},{"id":"GO:1904728","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0044381","count":1}]},{"hash":"1805360947371017436","title":"Organellar RNA Processing and Respiration","description":"The terms cluster around RNA processing in chloroplasts and mitochondria, plus mitochondrial ribosome assembly and overall cellular respiration, suggesting a group tied to organellar gene expression and energy production. The xenobiotic transport term is less connected but does not override the main theme. ","confidence":"Medium","size":12,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010207","count":1},{"id":"GO:1901259","count":1},{"id":"GO:0000963","count":1},{"id":"GO:0045333","count":1},{"id":"GO:1902775","count":1}]},{"hash":"1185933157196588566","title":"Calcium-dependent cell adhesion and developmental signaling","description":"This cluster centers on calcium-mediated cell-cell adhesion and calcium signaling (e.g., calcium-dependent adhesion and ER calcium regulation) and includes developmental and morphogenesis terms (ectoderm development, Wnt signaling regulation, cell migration). The cardiac conduction-related terms and adhesion in cardiac contexts further support a theme of calcium-regulated signaling and adhesion guiding development and tissue organization. The mitotic cytokinesis term may reflect coordination between cell cycle and adhesion dynamics, but the dominant theme is calcium-dependent adhesion coupled with developmental signaling.","confidence":"Medium","size":11,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1904798","count":3},{"id":"GO:0086019","count":3},{"id":"GO:0071255","count":3},{"id":"GO:0032471","count":3},{"id":"GO:0086073","count":3}]},{"hash":"286916708033978961","title":"Ubiquitination and ERAD-related proteins","description":"The strongest signals are protein autoubiquitination and the (obsolete) ubiquitin-dependent ERAD pathway, pointing to a cluster of proteins involved in ubiquitin-mediated proteostasis and endoplasmic reticulum-associated degradation. Other listed terms are broad or deprecated, but the ubiquitination/ERAD theme is the most coherent across the set.","confidence":"High","size":11,"edges":10,"triangles":6,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0055114","count":2},{"id":"GO:1902475","count":1},{"id":"GO:0008152","count":1}]},{"hash":"1408378645277007153","title":"Ubiquitin-Dependent Protein Degradation (ERAD)","description":"These proteins cluster around ubiquitin signaling and proteostasis, including ubiquitin-dependent ERAD, K63-linked ubiquitination, and autoubiquitination, suggesting a role in targeted protein degradation and quality control. While a few GO terms relate to stress responses (ethanol, chitin, glucocorticoids), the dominant theme is ubiquitin-mediated proteolysis and ER-associated degradation.","confidence":"High","size":11,"edges":30,"triangles":21,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:0030579","count":5},{"id":"GO:0030433","count":5},{"id":"GO:0090035","count":4},{"id":"GO:0070534","count":4},{"id":"GO:0051865","count":4}]},{"hash":"1277602336787321523","title":"Translational Control and mRNA Decay","description":"This cluster is dominated by translation-related terms (translation, initiation, termination, elongation, cytoplasmic translation) and mRNA decay (deadenylation-dependent decay), including selenocysteine incorporation, pointing to a cohesive theme of translational regulation and mRNA turnover. A couple of terms like glial proliferation and antibiotic response may be incidental annotations. There are no edges, consistent with a tightly focused functional set. ","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000288","count":2},{"id":"GO:0006413","count":2},{"id":"GO:0006415","count":2},{"id":"GO:0014009","count":2}]},{"hash":"1036525897076703392","title":"Ribosome biogenesis and translation","description":"The cluster is dominated by GO terms for ribosome assembly and function, including translation (cytoplasmic), ribosomal subunit biogenesis, and export of ribosomal subunits, with supporting signals from tRNA modification. These points strongly indicate involvement in the protein synthesis machinery and ribosome biogenesis, with secondary associations to cellular stress and cell cycle states.","confidence":"High","size":11,"edges":36,"triangles":77,"max_degree":8,"top_function":"cytoplasmic translation","top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0002181","count":3},{"id":"GO:0042254","count":3},{"id":"GO:0042274","count":3},{"id":"GO:0000055","count":2}]},{"hash":"1046039339065136949","title":"Steroid and lipid biosynthesis","description":"Proteins in this cluster show enrichment in steroid-related pathways (androgen metabolic and catabolic processes, glucocorticoid biosynthesis) and lipid-related biosynthesis (fatty acid elongation, mycolic acid biosynthesis) as well as pigment biosynthesis (melanin) and related metabolic processes (acetoin catabolism, PHB biosynthesis). While there are ancillary terms like lung development and transcription regulation, the strongest cohesive signal is synthesis and metabolism of steroids and lipids, suggesting a lipid/steroid biosynthesis theme for the cluster.","confidence":"Medium","size":11,"edges":40,"triangles":87,"max_degree":9,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0008209","count":10},{"id":"GO:0006355","count":10},{"id":"GO:0006710","count":10},{"id":"GO:0030324","count":10},{"id":"GO:0045150","count":10}]},{"hash":"1689368443618672176","title":"Ubiquitination and ERAD-Mediated Protein Degradation","description":"The cluster is dominated by ubiquitination-related terms (K63-linked ubiquitination, protein autoubiquitination) and the ubiquitin-dependent ERAD pathway, pointing to a shared role in protein tagging and ER-associated degradation; other terms are less central to this theme.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070534","count":8},{"id":"GO:0051865","count":8},{"id":"GO:0030433","count":8},{"id":"GO:0090035","count":6},{"id":"GO:0071361","count":6}]},{"hash":"2299414325486640561","title":"Embryonic Development and Cell Proliferation","description":"This cluster centers on developmental processes (neural tube closure, forebrain and skeletal development, multicellular organism development) and essential cell-cycle activities (DNA replication, DNA-templated transcription, mitotic cell cycle), suggesting a theme of development coupled with cell proliferation. A few stress/defense terms appear, likely reflecting ancillary cellular stress responses in these contexts.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0006351","count":6},{"id":"GO:0001843","count":5},{"id":"GO:0050830","count":5},{"id":"GO:0001403","count":5}]},{"hash":"2105067116960561931","title":"Developmental Differentiation and Cell Migration","description":"This cluster pulls together GO terms related to developmental differentiation (neural and skin lineages like midbrain dopaminergic neuron differentiation and hair follicle placode formation) and cell movement (cell migration, pseudopodium assembly) along with general regulatory processes (Wnt signaling inhibition, apoptosis, transcription regulation). The common thread is development-driven differentiation accompanied by cellular movement; hence this label. Some terms are peripheral, but they still contribute to the overarching theme of developmental change with migration. ","confidence":"Medium","size":11,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0008285","count":7},{"id":"GO:0016477","count":6},{"id":"GO:0090090","count":6},{"id":"GO:0043065","count":6},{"id":"GO:0060789","count":6}]},{"hash":"138492420865486764","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning cell cycle, ribophagy, synapse organization, sterol biosynthesis regulation, nuclear mRNA and tRNA export, calcium-regulated muscle contraction, and various regulatory processes. With only one edge and no clear shared pathway, there is no single unifying function to label this cluster. Thus Unknown.","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0007049","count":2},{"id":"GO:0034517","count":1},{"id":"GO:0050808","count":1},{"id":"GO:0032443","count":1},{"id":"GO:2000238","count":1}]},{"hash":"769757810997520052","title":"Rho/Rac-Driven Actin Remodeling and Cell Migration","description":"The top GO terms cluster around regulation of Rho and Rac signaling, actin cytoskeleton organization, and assembly of filopodia/lamellipodia, all linked to cell migration. Although heart development and cytokine responses appear, the common theme is cytoskeletal dynamics governed by Rho/Rac pathways that drive protrusion formation and movement.","confidence":"High","size":11,"edges":15,"triangles":5,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":3},{"id":"GO:0051489","count":3},{"id":"GO:0007507","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0030036","count":2}]},{"hash":"2187370676424694593","title":"Ubiquitin-dependent proteolysis and cell-cycle regulation","description":"The cluster repeatedly features ubiquitin-related processes (ubiquitin-dependent protein catabolic process, ERAD, autoubiquitination) and cell-cycle regulation terms, suggesting the proteins function together in targeted protein degradation and control of proliferative/division events. Additional terms on phosphorylation, septation and budding growth support a role in signaling and morphogenesis tied to cell-cycle progression.","confidence":"High","size":11,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":2},{"id":"GO:0030433","count":2},{"id":"GO:2000100","count":2},{"id":"GO:0042327","count":2},{"id":"GO:0031031","count":2}]},{"hash":"848176714778935469","title":"Broad amino acid and sugar metabolism","description":"Top GO terms reveal a mix of amino acid metabolism (e.g., L-alanine, L-valine, L-tyrosine biosynthesis/catabolism) and sugar-related pathways (pentose, pentose-phosphate shunt, inositol, galactarate, formate). With only a single edge and no cohesive single function, the cluster seems to reflect general metabolic processing of diverse carbon sources rather than a specific pathway. Therefore, a broad label like \"Broad amino acid and sugar metabolism\" best captures the shared theme without overclaiming a precise function.","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0009097","count":1},{"id":"GO:0019322","count":1},{"id":"GO:0046392","count":1},{"id":"GO:0042183","count":1}]},{"hash":"1756070604380734832","title":"Nitrosative Stress Response and Redox Modifications","description":"The cluster includes terms tied to nitrosative stress and redox-related protein modifications (peptidyl-cysteine S-nitrosylation, response to nitrosative stress) and copper ion response, alongside a few metabolism-related terms (mitochondrial translation, various sugar metabolism processes). This suggests a theme around redox stress responses and related post-translational modifications, with additional metabolic context, rather than a single well-defined pathway. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0032543","count":1},{"id":"GO:0033498","count":1},{"id":"GO:0019595","count":1},{"id":"GO:0006069","count":1}]},{"hash":"192767766151233217","title":"Cell Cycle and Mitosis Regulation","description":"The terms show enrichment for cell proliferation, spindle localization, metaphase alignment, and G1/S transition, with related cytoskeletal remodeling and EMT signals, pointing to a core function in cell division control and mitotic regulation.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":2},{"id":"GO:0010636","count":1},{"id":"GO:0051310","count":1},{"id":"GO:0030719","count":1},{"id":"GO:0030509","count":1}]},{"hash":"1831286517702918390","title":"Transmembrane transport of diverse molecules","description":"This cluster is dominated by GO terms describing movement of various compounds across membranes, including monoatomic anion transmembrane transport, xenobiotic export, long-chain fatty acid import into peroxisomes, teichoic acid and bacteriocin transport/immunity, oligopeptide export from mitochondria, ceramide translocation, and taurine transport. Together these point to a shared function in transmembrane transport across different membranes and substrates. An outlier term for nucleotide-excision repair is present but does not define the cluster. The sparse connectivity (low degree/ few edges) aligns with a broad transport-focused group rather than a single complex. Confidence reflects the clear transport theme with a minor annotation noise. ","confidence":"High","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0099133","count":3},{"id":"GO:0046618","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0015910","count":2},{"id":"GO:0015777","count":2}]},{"hash":"144862790095001466","title":"Ion transport and excitation-contraction signaling","description":"The cluster\u2019s GO terms are dominated by ion transport across membranes (calcium, sodium, potassium, manganese), regulation of skeletal muscle and heart contraction, mitochondrial calcium homeostasis, and neural signaling (synaptic potentiation, cell communication). This points to proteins involved in membrane ion handling that influence muscle contraction and neuronal signaling, with a possible outlier term related to melanin biosynthesis. ","confidence":"Medium","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048022","count":1},{"id":"GO:0098735","count":1},{"id":"GO:0010163","count":1},{"id":"GO:0060291","count":1},{"id":"GO:0051560","count":1}]},{"hash":"1597793816399283877","title":"Unknown","description":"The set mixes very different GO terms: vacuolar acidification and proton transport suggest membrane/ion handling; rRNA maturation hints at ribosome biogenesis; and several terms describe amino acid biosynthesis/catabolism (proline, lysine, alanine, putrescine) and porphyrin biosynthesis, plus GABA catabolism. With no clear shared function or interaction pattern (and zero edges/triangles), there isn\u2019t a coherent theme to name a specific cluster label beyond Unknown.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007035","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0000469","count":1},{"id":"GO:0009450","count":1}]},{"hash":"418714696186655986","title":"Cardiac-vascular signaling and development","description":"The cluster\u2019s top GO terms cluster around heart development and cardiac muscle hypertrophy, as well as branching morphogenesis of blood vessels. They are enriched for signaling functions (activation of adenylate cyclase, regulation of guanylate cyclase) and broader stress-responsive processes (xenobiotic response, apoptotic regulation, proliferation), suggesting a coherent theme of cardiac and vascular development with shared signal-transduction pathways. The long-term synaptic potentiation term is less central but may reflect common signaling cascades. Confidence: Medium","confidence":"","size":11,"edges":44,"triangles":112,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007190","count":7},{"id":"GO:0001569","count":7},{"id":"GO:0060291","count":7},{"id":"GO:0007507","count":7},{"id":"GO:0035690","count":7}]},{"hash":"1431401262752019659","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006886","count":2},{"id":"GO:0035023","count":2},{"id":"GO:0071039","count":1},{"id":"GO:0034473","count":1},{"id":"GO:0071035","count":1}]},{"hash":"22444568010249140","title":"RNA Pol II Transcription Regulation","description":"Based on the top GO terms, this cluster centers on RNA polymerase II\u2013mediated transcription, including DNA-templated transcription, transcription elongation, and negative regulation of transcription by RNAP II. Some terms also touch on chromatin/nucleosome density and protein interactions, and a few terms reference oxidative stress and ER-Golgi processes, suggesting ancillary roles for a multifunctional set of proteins. Given the strong representation of RNAP II\u2013related transcription terms, the label RNAP II Transcription Regulation captures the core function.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0017004","count":2},{"id":"GO:0034599","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0060303","count":2}]},{"hash":"84224577817381296","title":"Nuclear Import of Ribosomal Proteins","description":"This cluster is dominated by GO terms for importing proteins into the nucleus, notably NLS-bearing proteins and ribosomal proteins. The prominence of these two related terms suggests a shared function in nuclear import/transport tied to ribosome biogenesis, with other, less cohesive terms providing additional context but not overriding the main theme.","confidence":"Medium","size":11,"edges":19,"triangles":10,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0006607","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0006610","count":4},{"id":"GO:1904798","count":3},{"id":"GO:0086019","count":3}]},{"hash":"814391618595265959","title":"Proteostasis and vesicle trafficking","description":"The cluster is enriched for ubiquitin-dependent protein catabolic processes, proteasome assembly, and cellular responses to misfolded proteins, along with transport-related GO terms such as endosome-to-vacuole transfer, intracellular protein transport, and exosome assembly regulation. These together point to coordinated protein quality control and vesicular trafficking pathways. Some plant-specific terms appear as outliers, but the dominant signal aligns with proteostasis and trafficking functions.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006511","count":2},{"id":"GO:0035520","count":1},{"id":"GO:0045324","count":1},{"id":"GO:0048317","count":1},{"id":"GO:0043248","count":1}]},{"hash":"308408655498583676","title":"Vertebrate neural development and transcriptional regulation","description":"This cluster is dominated by neural and vertebrate development terms (forebrain development, neural tube closure, skeletal system development) and by transcription-related processes (DNA-templated transcription, mitotic cell cycle), suggesting a group of proteins involved in developmental programs with transcriptional control. Some immune or stress-related terms appear, indicating additional stress responses that may accompany development or reflect broader cellular contexts. Overall, the theme centers on neural development with transcriptional regulation.","confidence":"Medium","size":11,"edges":7,"triangles":2,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030900","count":6},{"id":"GO:0001843","count":6},{"id":"GO:0050830","count":6},{"id":"GO:0071276","count":6},{"id":"GO:0070059","count":6}]},{"hash":"1324087443585585227","title":"Membrane transport of ions and nutrients (vacuolar)","description":"The top GO terms are dominated by transmembrane transport of various ions and small metabolites (phosphate, nitrate/nitrite, sodium, arabinose) and nutrient processing (nitrate assimilation, fucose metabolism). The presence of vacuole-related terms (microautophagy, vacuole fusion) suggests a connection to vacuolar transport and trafficking. Taken together, the proteins likely comprise a set of membrane transporters involved in nutrient and ion uptake and vacuolar nutrient handling, with auxiliary vacuolar processes.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":3},{"id":"GO:0016237","count":2},{"id":"GO:0042144","count":2},{"id":"GO:0015706","count":2},{"id":"GO:0015751","count":2}]},{"hash":"686769592844096471","title":"Amino-Acid and Lipid Catabolism with Quinone Biosynthesis","description":"This cluster shows multiple catabolic processes (phenylacetate, valine, GABA, putrescine) along with fatty acid beta-oxidation, and includes biosynthesis of quinones (phylloquinone and menaquinone), suggesting a metabolic module focused on energy generation and cofactor production; antibiotic biosynthesis is less central but fits within secondary metabolism.","confidence":"Medium","size":11,"edges":52,"triangles":140,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0010124","count":4},{"id":"GO:0006635","count":4},{"id":"GO:0042372","count":4},{"id":"GO:0006574","count":4}]},{"hash":"973143635164546138","title":"Unknown","description":"The terms are a scattered mix of biosynthetic (anthocyanin, antibiotic, poly-hydroxybutyrate), catabolic (uracil, 3-phenylpropionate), nutrient/response processes (nitrogen utilization, response to toxic substance), and even chromatin-related activity, with no clear shared function tying the proteins together. The edges are zero, reinforcing that there isn\u2019t a coherent biological theme for this cluster.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902987","count":2},{"id":"GO:0009718","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0006212","count":2}]},{"hash":"2006085448346974454","title":"Steroid and lipid biosynthesis pathways","description":"The top GO terms center on biosynthetic processes for steroids (androgen- and glucocorticoid-related) and lipids (fatty acid elongation, mycolic acid), with additional biosynthesis terms for antibiotics and melanin. This points to a core theme of steroid- and lipid-related biosynthesis, with some broader metabolite biosynthesis signals. Confidence: Medium","confidence":"Medium","size":11,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0017000","count":6},{"id":"GO:0008209","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0006710","count":4},{"id":"GO:0030324","count":4}]},{"hash":"1827320688038398320","title":"Antiviral Innate Immunity and Interferon Response","description":"The cluster shows strong enrichment for innate immune response, cellular response to type I interferon, and dsRNA-related antiviral defense, suggesting a core function in antiviral immunity. While some terms touch on development or cell division, these likely reflect broader annotation or secondary roles; the dominant pattern is antiviral defense signaling.","confidence":"High","size":11,"edges":30,"triangles":25,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0045087","count":5},{"id":"GO:0071357","count":5},{"id":"GO:0051301","count":5},{"id":"GO:0006463","count":5},{"id":"GO:0055059","count":5}]},{"hash":"2302568468285340405","title":"Developmental Differentiation and Maturation","description":"This cluster centers on processes that guide cell fate decisions and maturation across different lineages, including neuron maturation, erythrocyte differentiation, and regulation of stem cell proliferation. Epigenetic regulation terms (histone methylation) and metabolic support (thiamine biosynthesis) further fit the theme of developmental control and maturation. Despite the lack of a single direct pathway connecting all proteins, the common thread is developmental differentiation and maturation signals. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042551","count":5},{"id":"GO:2000648","count":5},{"id":"GO:0045793","count":5},{"id":"GO:0046886","count":4},{"id":"GO:0009228","count":4}]},{"hash":"1344713262257781756","title":"Nucleolar transcription and ribosome biogenesis","description":"The cluster centers on frequent GO terms for ribosome biogenesis, nucleolar rRNA transcription, nucleologenesis, and broad transcription by RNA polymerases I-III, all pointing to nucleolar transcriptional activities and ribosome assembly, with related cell cycle involvement. The presence of multiple transcriptional processes alongside ribosome-related terms supports a cohesive nucleolar/ribosome biogenesis theme, despite some outliers like regenerative ncRNA heterochromatin formation and hepatocyte apoptosis.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0007049","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0042790","count":2},{"id":"GO:0017126","count":2}]},{"hash":"242908870288825182","title":"Vesicle trafficking and synaptic vesicle dynamics","description":"The cluster is enriched for GO terms describing ER-to-Golgi transport, endosome-to-Golgi and endosome-to-late endosome traffic, Golgi organization, and processes tied to neurotransmitter handling (e.g., spontaneous secretion, long-term potentiation, and vesicle recycling). Together these terms point to a coherent module of intracellular membrane trafficking with a focus on synaptic vesicle dynamics and surface protein localization.","confidence":"High","size":11,"edges":10,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006888","count":5},{"id":"GO:0034498","count":5},{"id":"GO:0032258","count":5},{"id":"GO:0045022","count":5},{"id":"GO:1903078","count":5}]},{"hash":"2128482919243764894","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":3},{"id":"GO:0006515","count":2},{"id":"GO:0009443","count":2},{"id":"GO:0016310","count":2},{"id":"GO:0009229","count":2}]},{"hash":"251149003285956978","title":"Developmental Growth and Tissue Remodeling","description":"This cluster centers on organ development and tissue remodeling, with GO terms like pancreas morphogenesis, multicellular organism growth, elastin catabolic process, and smooth muscle cell migration, suggesting a shared role in growth regulation and ECM remodeling rather than a single signaling pathway. Some regulatory/immune terms are present but do not redefine the main theme.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0006067","count":2},{"id":"GO:0061668","count":2},{"id":"GO:0045415","count":1},{"id":"GO:0050720","count":1}]},{"hash":"404593200971566185","title":"Nucleolar transcription and ribosome biogenesis","description":"The top GO terms are dominated by ribosome biogenesis and nucleolar transcription (including RNA polymerases I, II, and III, and RNA-templated transcription), indicating these proteins are mainly involved in nucleolar transcriptional activity and ribosome assembly. Some outliers (peroxisomal import, DNA replication, translesion synthesis) show additional functions but do not outweigh the core theme. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0042790","count":1},{"id":"GO:1904750","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0042797","count":1}]},{"hash":"1266532951853146811","title":"Translation preinitiation complex assembly","description":"Top GO terms are dominated by translation-related processes: GO:0001731 (formation of translation preinitiation complex) and GO:0002188 (translation reinitiation) together with GO:0070208 (protein heterotrimerization), which points to assembly of initiation factor subunits (e.g., eIF2/eIF3 complexes). This suggests the cluster groups proteins involved in initiating translation and reinitiation, potentially regulated by the GCN2 pathway and other control mechanisms (SCF ubiquitin-dependent proteolysis). While a few terms relate to forebrain/skeletal development, the strongest signals pertain to translation initiation, supporting the chosen label. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0070208","count":4},{"id":"GO:0001731","count":4},{"id":"GO:0002188","count":4},{"id":"GO:0048705","count":3},{"id":"GO:0031146","count":3}]},{"hash":"1881211710379878955","title":"Vesicle trafficking and cell polarity","description":"The dominant signals are vesicle trafficking and polarity: vesicle docking in exocytosis, regulation of the secretory pathway, and adherens junction organization, with additional hints from cell polarity maintenance and spine morphogenesis. Some terms (e.g., subtelomeric heterochromatin formation) appear less connected, but do not dominate the cluster\u2019s theme. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071805","count":3},{"id":"GO:0006904","count":3},{"id":"GO:0006348","count":2},{"id":"GO:0061001","count":2},{"id":"GO:1990456","count":2}]},{"hash":"2120613896967907187","title":"Neural signaling and sensory processing","description":"The proteins are linked to neuronal communication and sensory/behavioral responses: cholinergic synaptic transmission, excitatory postsynaptic potentials, norepinephrine secretion, and sensory perception of sound, along with reflexes like the righting reflex and conditioned taste aversion. A few terms (e.g., DNA-templated transcription, response to amino acids) are less central, but the dominant theme is neural signaling and sensory processing, supporting this label.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0001988","count":1},{"id":"GO:2000344","count":1},{"id":"GO:0043200","count":1},{"id":"GO:0001661","count":1}]},{"hash":"2220389174245449947","title":"Viral infection and host interaction proteins","description":"Although the cluster contains a mix of GO terms, several key items point to viral life cycle and virus-host interplay: virion assembly, establishment of proviral latency, viral release from host cell, host-mediated activation of viral genome replication, and symbiont entry into host. Additional terms like leukocyte migration reflect host immune responses, while the NAD+ catabolic process and protein folding terms are less central. Overall, the dominant theme is proteins involved in viral infection and host interactions.","confidence":"Medium","size":11,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019677","count":2},{"id":"GO:2000276","count":1},{"id":"GO:0019068","count":1},{"id":"GO:0048453","count":1},{"id":"GO:0075713","count":1}]},{"hash":"2299810486265461942","title":"Protein and amino acid acetylation","description":"The cluster is dominated by GO terms describing acetylation events (N-terminal, peptidyl-lysine, spermine, glutamic acid), along with related acetyl-CoA\u2013dependent metabolic processes, suggesting a cohesive function around acetylation chemistry and regulation.","confidence":"High","size":11,"edges":55,"triangles":165,"max_degree":10,"top_function":null,"top_go_terms":[{"id":"GO:0009447","count":11},{"id":"GO:0018003","count":11},{"id":"GO:2000025","count":11},{"id":"GO:0006044","count":11},{"id":"GO:0032919","count":11}]},{"hash":"1858999742061964762","title":"Nucleotide Transport and DNA Maintenance","description":"The proteins seem to cluster around core genome-maintenance activities (DNA repair and DNA-templated transcription) together with recurring nucleobase transport activities (hypoxanthine, urate, guanine, xanthine). While some terms like brain development are broader, the dominant pattern ties nucleotide handling and DNA-related processes, suggesting a combined theme of nucleotide transport and genome maintenance.","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006281","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0035344","count":1}]},{"hash":"1516716076005784348","title":"Mitochondrial Transport and Membrane Potential Regulation","description":"The terms cluster around transport of metabolites and ions across mitochondrial membranes (ADP/ATP, alpha-ketoglutarate, magnesium), and regulation of membrane permeability and membrane potential, all pointing to mitochondrial energy metabolism. A few terms (heme transport, insulin/IGF signaling) are peripheral but do not override the core mitochondrial transport theme.","confidence":"High","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015886","count":2},{"id":"GO:0048714","count":2},{"id":"GO:0046902","count":1},{"id":"GO:0051881","count":1},{"id":"GO:0015742","count":1}]},{"hash":"1241480212085287144","title":"Unknown","description":"The top GO terms span sensory perception, RNA processing (5S rRNA maturation, spliceosome assembly), protein quality control (negative regulation of protein refolding, ubiquitin-dependent proteolysis), GPCR complex assembly, and plant developmental processes (cotyledon vascular tissue patterning), with no single cohesive biological theme linking them all. This diversity suggests no clear, representative function for the cluster, so the label Unknown is most appropriate.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":1},{"id":"GO:0000481","count":1},{"id":"GO:1902605","count":1},{"id":"GO:0007329","count":1},{"id":"GO:0001938","count":1}]},{"hash":"307729134754502262","title":"Endosome dynamics and neural signaling","description":"This cluster centers on receptor recycling and regulation of endosome size, plus glutamatergic synaptic transmission, pointing to neural endomembrane trafficking and signaling. Additional terms for Rho signaling and transcription/chromatin remodeling suggest a broader link to activity-dependent gene regulation in neurons, though some obsolete terms appear as noise. ","confidence":"Medium","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0001881","count":6},{"id":"GO:0051036","count":6},{"id":"GO:0035023","count":6},{"id":"GO:0035249","count":6},{"id":"GO:0006355","count":6}]},{"hash":"1806992718168650722","title":"Unknown","description":"The top GO terms are a mix of LDL receptor\u2013related lipid metabolism processes and peptide/prohormone processing, along with some developmental terms. There isn\u2019t a single coherent functional theme tying all terms together, so a specific, intuitive label isn\u2019t supported by the data.","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1905596","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0090472","count":1},{"id":"GO:0007354","count":1},{"id":"GO:0001920","count":1}]},{"hash":"2134862036610750444","title":"Unknown","description":"Unknown","confidence":"","size":11,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036155","count":2},{"id":"GO:0019433","count":2},{"id":"GO:2000124","count":2},{"id":"GO:0019647","count":1},{"id":"GO:0005975","count":1}]},{"hash":"2163192200702447620","title":"Lipid metabolism and ER-Golgi transport","description":"The cluster\u2019s top GO terms strongly point to lipid-related metabolism (sphingomyelin catabolic process, lipid A biosynthetic process, mevalonate pathway) and vesicle trafficking between the ER and Golgi, suggesting a group of proteins involved in membrane lipid handling and the secretory pathway. Some terms are older/obsolete or reflect broader stress responses, but the core signals fit lipid metabolism plus membrane trafficking. ","confidence":"Medium","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001569","count":10},{"id":"GO:0016576","count":10},{"id":"GO:0035690","count":10},{"id":"GO:1900486","count":10},{"id":"GO:0006685","count":10}]},{"hash":"228515751675161682","title":"Adipocyte lipid and sphingolipid biosynthesis","description":"This cluster centers on fatty acid and sphingolipid biosynthesis (e.g., monounsaturated fatty acids, sphinganine/sphingosine) and includes white fat cell differentiation, indicating adipocyte lipid metabolism and adipogenesis as the shared theme.","confidence":"High","size":10,"edges":11,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006667","count":5},{"id":"GO:0050872","count":5},{"id":"GO:0010205","count":5},{"id":"GO:0070542","count":5},{"id":"GO:0034435","count":5}]},{"hash":"488593200545452749","title":"Bacterial cell wall biosynthesis and division","description":"The top terms cluster around cell wall organization, peptidoglycan and glycolipid biosynthesis, and cell cycle/division, with some related to cell shape regulation and antibiotic metabolism. This points to a cohesive theme of bacterial cell wall construction and the associated cell division processes, despite a few miscellaneous metabolic terms present. ","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":3},{"id":"GO:0006212","count":2},{"id":"GO:0030259","count":2},{"id":"GO:0016999","count":2},{"id":"GO:0005975","count":2}]},{"hash":"2287053156435726279","title":"Unknown","description":"The top GO terms cover a mix of detoxification, immune response, vitamin and core metabolic processes, and various developmental pathways (neuronal and erythrocyte differentiation, stem cell proliferation). There isn't a single coherent biological theme tying these terms together, so a concise, representative label cannot be determined.","confidence":"","size":10,"edges":15,"triangles":7,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":3},{"id":"GO:0032496","count":3},{"id":"GO:0046886","count":3},{"id":"GO:0045648","count":3},{"id":"GO:0009228","count":3}]},{"hash":"1017007258354766819","title":"RNA Pseudouridine Synthesis Enzymes","description":"The GO terms are dominated by RNA modification activities, with strong signals for tRNA and rRNA pseudouridine synthesis, suggesting the cluster\u2019s core function is RNA modification enzymes; the other metabolic terms appear incidental or broad annotations that do not define a cohesive alternative theme.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031119","count":2},{"id":"GO:0000455","count":2},{"id":"GO:0009236","count":1},{"id":"GO:0006461","count":1},{"id":"GO:0010167","count":1}]},{"hash":"1304309995470169088","title":"Ribosome biogenesis and translation","description":"The top GO terms cluster tightly around ribosome production and function: ribosomal large subunit export from the nucleus, ribosome biogenesis, cytoplasmic translation, and protein homooligomerization. These indicate a core theme of ribosome assembly and protein synthesis, with cell cycle/division terms reflecting growth coordination with ribosome capacity. A few terms (endocytic recycling, stress response regulation, GABAergic signaling) are peripheral but do not override the central ribosome/translation theme.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0051260","count":6},{"id":"GO:0000055","count":6},{"id":"GO:0051301","count":6},{"id":"GO:0007049","count":6},{"id":"GO:0042254","count":5}]},{"hash":"25581759243821934","title":"Ubiquitin-Mediated Regulation and Mitotic Checkpoints","description":"Proteins in this cluster show strong representation of ubiquitination-related terms (protein autoubiquitination; ubiquitin-dependent ERAD pathway; ubiquitin ligase activity regulation) and mitotic DNA damage checkpoint signaling (G1 and G2). This suggests a cohesive role in ubiquitin-dependent protein turnover that influences cell cycle progression and DNA damage responses, with ancillary signals for transcription and stress responses such as ethanol and cadmium exposure.","confidence":"Medium","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0071361","count":8},{"id":"GO:0051865","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0046827","count":6},{"id":"GO:0031571","count":6}]},{"hash":"1799106700369187485","title":"Heat-stress\u2013related protein folding and quality control","description":"This cluster is dominated by GO terms for response to heat, unfolded protein response, ER protein folding, and ubiquitin-proteasome\u2013mediated quality control, which together point to a shared role in maintaining protein folding and turnover under thermal stress. While a few terms relate to DNA replication and developmental signaling, the core theme centers on proteostasis and stress-induced protein maturation/degradation.","confidence":"High","size":10,"edges":38,"triangles":85,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":5},{"id":"GO:0006260","count":5},{"id":"GO:1900035","count":5},{"id":"GO:1901621","count":5},{"id":"GO:0034975","count":5}]},{"hash":"100982721237569371","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":37,"triangles":71,"max_degree":9,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043547","count":6},{"id":"GO:0060271","count":5},{"id":"GO:0050709","count":5},{"id":"GO:0006547","count":5},{"id":"GO:0007117","count":5}]},{"hash":"1834112995909925057","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":26,"triangles":36,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0071441","count":2},{"id":"GO:0001178","count":2},{"id":"GO:1990417","count":2},{"id":"GO:0071035","count":2}]},{"hash":"108762210346105442","title":"Xenobiotic Response and Vitamin Metabolism","description":"Top GO terms indicate responses to external compounds (xenobiotics, herbicides, selenium) alongside vitamin and cofactor metabolism (thiamine, tetrahydrofolate) and related metabolic regulation, with no observed protein\u2013protein edges. This suggests a broad, multi-functional set centered on detox-related signaling and metabolic processes, enough to warrant a concise label capturing both xenobiotic response and vitamin metabolism.","confidence":"Low","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071320","count":3},{"id":"GO:0045648","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0010269","count":3}]},{"hash":"1684080559714124281","title":"ER Protein Folding and Unfolded Protein Response","description":"The strongest shared functional theme among the top GO terms is protein folding in the endoplasmic reticulum and the cellular response to unfolded proteins, accompanied by a heat-shock/ER-stress context (GO:0034975, GO:0006986, GO:0009408). These indicate a proteostasis/ER stress response cluster, with other terms like translational frameshifting and protein complex oligomerization likely reflecting broader cellular quality-control processes. Overall, the data support a cohesive theme around ER-associated protein folding and stress response rather than a single other pathway.","confidence":"High","size":10,"edges":20,"triangles":10,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0032869","count":2},{"id":"GO:0009408","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1900035","count":2},{"id":"GO:1901621","count":2}]},{"hash":"573716144554909590","title":"Unknown","description":"The top GO terms are diverse (insulin secretion, activin signaling, heart morphogenesis, redox response, neural activity, hydrogen peroxide, and cell division), with only two occurrences each, so there is no clear shared function to name.","confidence":"","size":10,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030073","count":2},{"id":"GO:0032925","count":2},{"id":"GO:1901710","count":2},{"id":"GO:0055010","count":2},{"id":"GO:0051775","count":2}]},{"hash":"1480740407959842752","title":"NF-kB-Mediated Innate Immune Regulation","description":"Dominant theme is NF-kB signaling and innate antiviral defense, supported by terms like positive regulation of canonical NF-kappaB signaling, I-kappaB phosphorylation, defense response to virus, and innate immune response. Additional terms indicate transcriptional and kinase activity regulation, consistent with tight control of immune signaling; a few terms hint at calcium-related signaling and neuronal development, but the core cluster centers on NF-kB\u2013driven immune regulation.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0030433","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0043123","count":2}]},{"hash":"2225201259931205768","title":"Sugar and osmolyte transport","description":"The GO terms prominently indicate transport activities for glucose, trehalose, urate, dehydroascorbic acid, organic anions, and fructose, as well as a cellular response to osmotic stress. This suggests a cohesive function centered on moving small metabolites and osmolytes across membranes, with stress-related regulation. Some terms like plasmid maintenance and mitochondrial distribution appear incidental and do not redefine the core theme.","confidence":"Medium","size":10,"edges":17,"triangles":3,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006276","count":1},{"id":"GO:0048311","count":1},{"id":"GO:1904728","count":1},{"id":"GO:0044381","count":1},{"id":"GO:0015747","count":1}]},{"hash":"266943344384082536","title":"Chromatin remodeling and transcription regulation","description":"The top GO terms point to transcription control by RNA polymerase II and transcription start site regulation, together with chromatin remodeling, indicating a cluster centered on gene expression regulation via chromatin state. Some metabolic terms (lipid catabolism, endocannabinoid signaling) are present but less representative, so the core theme is transcription regulation through chromatin dynamics.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0043044","count":2},{"id":"GO:0055114","count":2},{"id":"GO:2000124","count":2},{"id":"GO:0052651","count":2}]},{"hash":"2080527522156947750","title":"Metal ion transport and homeostasis","description":"This cluster is dominated by GO terms for transmembrane transport of multiple metal ions (copper, zinc, mercury, cadmium), including import/export and regulation, plus xenobiotic transport, pointing to a common function in metal ion handling and detoxification. The presence of a related oxidative stress term (superoxide metabolic process) aligns with metal-induced stress, supporting the homeostasis theme.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071577","count":1},{"id":"GO:0046689","count":1},{"id":"GO:0070574","count":1},{"id":"GO:0015680","count":1},{"id":"GO:0098705","count":1}]},{"hash":"1550988020688927599","title":"Unknown","description":"The terms show a scattered mix of regulatory processes (transcription, cell cycle, TLR signaling, endosome/ receptor trafficking) and a neuronal synaptic term, with no clear, cohesive function linking the proteins. Edges are absent and several terms are obsolete, making a specific, confident label unreliable.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001881","count":1},{"id":"GO:0051036","count":1},{"id":"GO:0035023","count":1},{"id":"GO:0035249","count":1},{"id":"GO:0006355","count":1}]},{"hash":"635085389393539654","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0061158","count":2},{"id":"GO:1904582","count":2},{"id":"GO:1904246","count":2},{"id":"GO:1904628","count":2}]},{"hash":"122241364997338322","title":"Unknown","description":"The terms are widely disparate, including carbohydrate catabolism, water transport regulation, aging, DNA- and cell cycle\u2013related processes, and corneocyte development, with no shared theme and no edges linking proteins, so there is no coherent functional label for the cluster.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019391","count":1},{"id":"GO:0000272","count":1},{"id":"GO:0005990","count":1},{"id":"GO:2001153","count":1},{"id":"GO:0007568","count":1}]},{"hash":"1485150167316251891","title":"Ribosome biogenesis and RNA processing","description":"Top GO terms show strong signals for rRNA maturation (SSU/LSU from tricistronic transcripts) and ribosomal large subunit biogenesis, along with mRNA splicing via the spliceosome. While some terms relate to DNA replication or transcription regulation, the dominant theme centers on ribosome assembly and RNA processing (including rRNA maturation and spliceosome-mediated splicing). This makes the suggested label a concise representation of the cluster\u2019s core function.","confidence":"High","size":10,"edges":14,"triangles":7,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0000462","count":5},{"id":"GO:0045944","count":5},{"id":"GO:0000463","count":5},{"id":"GO:0042273","count":5}]},{"hash":"1253707513125162597","title":"Mitochondrial Energy Metabolism","description":"This cluster is best described by energy-producing and cofactor-dependent pathways. The top GO terms point to mitochondrial NADH-to-ubiquinone electron transport, regulation of membrane potential, and various cofactor-related processes (lipoate metabolism, dihydrolipoamide metabolism, tetrahydrofolate metabolism), with supporting signals from amino acid catabolism and central carbon metabolism. While a few terms (aging, mercury detox, sperm capacitation) appear less central, the dominant theme ties to mitochondrial energy production and associated metabolic cofactor networks.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006096","count":3},{"id":"GO:0007568","count":2},{"id":"GO:0046653","count":2},{"id":"GO:0051068","count":2},{"id":"GO:0009106","count":2}]},{"hash":"660708608260356378","title":"Nuclear transcription machinery and spindle assembly","description":"This cluster is dominated by terms for RNA polymerase I/II/III assembly and transcription elongation regulation, indicating core transcription machinery. The presence of tubulin complex and mitotic spindle assembly terms suggests a link to microtubule dynamics during cell division, pairing nuclear transcription with mitotic architecture. A few transport and folding terms are present but appear ancillary to the main theme.","confidence":"Medium","size":10,"edges":14,"triangles":3,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0007021","count":2},{"id":"GO:0090307","count":2},{"id":"GO:0071806","count":2},{"id":"GO:0000060","count":2},{"id":"GO:1990115","count":1}]},{"hash":"923230822119212850","title":"ER Folding and Secretory Pathway Trafficking","description":"Most of the top terms center on endoplasmic reticulum processing\u2014unfolded protein response, ER-to-Golgi and Golgi vesicle transport, and protein folding/refolding\u2014pointing to a cluster of proteins involved in ER quality control and trafficking through the secretory pathway; a few terms appear as noise (e.g., viral replication, mitotic checkpoint) but do not dominate the cluster theme.","confidence":"High","size":10,"edges":17,"triangles":10,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0034214","count":8},{"id":"GO:0033314","count":8},{"id":"GO:0006888","count":8},{"id":"GO:0070389","count":8},{"id":"GO:0045041","count":8}]},{"hash":"1851294008951676225","title":"Neural development and embryogenesis","description":"The top GO terms strongly cluster around neural and embryonic development (neural tube closure, forebrain development, multicellular organism development) with supporting roles in transcriptional regulation and cell cycle. Although stress and defense responses appear (ER stress\u2013induced apoptosis, cadmium response, Gram-positive defense), the most represented and coherent theme is development and neural formation, implying these proteins function together in neural development and associated transcriptional control.","confidence":"Medium","size":10,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001843","count":8},{"id":"GO:0050830","count":8},{"id":"GO:0001403","count":8},{"id":"GO:0000278","count":8},{"id":"GO:0007275","count":8}]},{"hash":"2135112626024530349","title":"Unknown","description":"The top GO terms span very different biological areas (sperm capacitation, DNA replication/repair, cell migration, various developmental processes, B cell signaling, apoptosis, and amino acid starvation response) with no clear, single unifying function. This lack of a cohesive theme makes a concise, representative label difficult, so Unknown is appropriate.","confidence":"","size":10,"edges":30,"triangles":43,"max_degree":9,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0048240","count":9},{"id":"GO:0006260","count":8},{"id":"GO:0006281","count":7},{"id":"GO:0016477","count":6},{"id":"GO:0010898","count":6}]},{"hash":"1323803015945074751","title":"Embryonic Development and Organogenesis","description":"The cluster's top GO terms are largely about development\u2014neural tube closure, corpus callosum development, and trachea formation\u2014along with related processes like cell migration and regulation of apoptosis, which are typical during tissue and organ formation. Although there are a few immune- or stress-related terms (B cell signaling, response to virus), the strongest signal centers on embryonic tissue formation, justifying a development-focused label.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0016477","count":6},{"id":"GO:0010898","count":6},{"id":"GO:0022038","count":6},{"id":"GO:0050853","count":6}]},{"hash":"642635857605707144","title":"RNA Processing and Transcription Regulation","description":"The top GO terms cluster around RNA metabolism (snoRNA release from pre-rRNA; rRNA catabolic process) and transcriptional start site regulation, with additional hints of post-transcriptional handling (stress granule localization) and general protein targeting. Together they point to a theme of RNA processing and control of gene expression, despite some obsolete annotations suggesting noise. This cluster seems to group proteins involved in RNA biogenesis and transcription regulation rather than a single, narrow pathway.","confidence":"Medium","size":10,"edges":24,"triangles":36,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0000160","count":4},{"id":"GO:0071441","count":3},{"id":"GO:0001178","count":3},{"id":"GO:1990417","count":3},{"id":"GO:0071035","count":3}]},{"hash":"1100266880726806073","title":"Mitochondrial lipid metabolism and transport","description":"This cluster centers on GO terms related to lipid management (cholesterol homeostasis, triglyceride biosynthesis regulation) and mitochondrial function (protein import into mitochondrial matrix, regulation of mitochondrial membrane permeability), suggesting a theme around lipid handling in mitochondria and associated transport processes. Some terms (suberin/ommochrome biosynthesis) point to lipid-derived biosynthesis, reinforcing a lipid/membrane\u2013associated theme, though several terms are peripheral. Confidence: Medium.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042632","count":2},{"id":"GO:0070940","count":1},{"id":"GO:0010867","count":1},{"id":"GO:1903740","count":1},{"id":"GO:0030150","count":1}]},{"hash":"1839341148596058467","title":"Membrane Transporters for Ions and Metabolites","description":"The top GO terms are dominated by transmembrane transport of diverse substrates (nitrate, nitrite, arabinose, sodium ions, phosphate, vitamins), along with related processes like nitrate assimilation and fucose metabolism. This strongly points to a cluster of membrane transporter proteins handling the movement of various solutes across membranes, with one related note on neurotransmitter loading into synaptic vesicles suggesting vesicle-associated transport. Overall, the common theme is solute transport across membranes.","confidence":"High","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":10},{"id":"GO:0015751","count":10},{"id":"GO:0015707","count":10},{"id":"GO:0042891","count":10},{"id":"GO:0035725","count":10}]},{"hash":"1678549986820326100","title":"Plant AGP glycoprotein biosynthesis and root hair development","description":"Most terms converge on plant-specific glycoprotein and cell wall biology (arabinogalactan protein metabolic process; poly-N-acetyllactosamine biosynthetic process; Lewis a epitope biosynthesis) and developmental processes such as root hair cell development and seed mucilage/coat formation. This pattern suggests the cluster represents plant cell wall glycoprotein biosynthesis, particularly arabinogalactan proteins, and associated root epidermal development.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0075015","count":1},{"id":"GO:0030311","count":1},{"id":"GO:0042248","count":1},{"id":"GO:0010405","count":1}]},{"hash":"1819567588412908995","title":"Neural development and axon guidance","description":"The cluster features GO terms tied to facial nerve and retinal development, neuronal migration, paranodal junctions, and axon guidance, pointing to a cohesive theme of neural development and axonal pathfinding. Although a couple terms relate to other processes, the dominant signals are neural and axon guidance related.","confidence":"High","size":10,"edges":36,"triangles":63,"max_degree":9,"top_function":null,"top_go_terms":[{"id":"GO:1903375","count":1},{"id":"GO:0060978","count":1},{"id":"GO:0021828","count":1},{"id":"GO:0002175","count":1},{"id":"GO:1902336","count":1}]},{"hash":"1285553140344321377","title":"Transcriptional Regulation and Inflammatory Signaling","description":"The terms show a core focus on transcriptional control by RNA polymerase II (both negative and positive regulation) and production of inflammatory cytokines (IL-1\u03b2, IL-8), with additional development and tissue remodeling processes (pancreas morphogenesis, elastin catabolism, smooth muscle migration). This suggests a functionally coherent group involved in regulating gene expression while contributing to developmental and inflammatory/remodeling contexts.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0045415","count":2},{"id":"GO:0050720","count":2},{"id":"GO:0060309","count":2},{"id":"GO:0035264","count":2}]},{"hash":"1007434182895368097","title":"Steroid and lipid biosynthesis and pigment production","description":"Based on the Top Terms, the cluster centers on biosynthetic processes: androgen metabolic and catabolic processes, glucocorticoid biosynthesis, fatty acid elongation, mycolic acid biosynthesis, poly-hydroxybutyrate biosynthesis, and melanin biosynthesis. This suggests a unifying theme around synthesis of lipids, steroids, and pigments across different organisms. Some terms like regulation of DNA-templated transcription and lung development appear incidental to this core theme, likely annotation noise rather than defining function. ","confidence":"Medium","size":10,"edges":5,"triangles":0,"max_degree":3,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0008209","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0006710","count":4},{"id":"GO:0030324","count":4},{"id":"GO:0045150","count":4}]},{"hash":"1295248673651030479","title":"Unknown","description":"The terms are very diverse, spanning insulin secretion, activin signaling, homoserine biosynthesis, heart morphogenesis, protein folding, redox response, histone isomerization, neuronal signaling, phosphatase regulation, and oxidative stress. There isn\u2019t a clear, singular function tying these together, so the cluster doesn\u2019t map to a cohesive, interpretable biological theme.","confidence":"","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0030073","count":1},{"id":"GO:0032925","count":1},{"id":"GO:1901710","count":1},{"id":"GO:0055010","count":1},{"id":"GO:0006457","count":1}]},{"hash":"370508715569545529","title":"Post-transcriptional RNA processing and translation control","description":"The cluster is strongly enriched for spliceosome-related activities (splicing regulation, spliceosome assembly, splice site recognition), mRNA processing/modification, and post-transcriptional control including ncRNA/miRNA-mediated silencing and translation initiation complex assembly, indicating a cohesive theme of RNA maturation and translation regulation rather than transcriptional control. The presence of a developmental term (blastocyst formation) likely reflects context-specific expression but does not override the dominant RNA-centric theme.","confidence":"High","size":10,"edges":45,"triangles":120,"max_degree":9,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0010610","count":8},{"id":"GO:0048026","count":6},{"id":"GO:0000381","count":5},{"id":"GO:0016556","count":5},{"id":"GO:0001825","count":5}]},{"hash":"1567212492963020472","title":"Mitochondrial transport and membrane potential regulation","description":"The cluster's terms center on mitochondrial membrane dynamics and transport: regulation of membrane permeability and potential, transport of key metabolites (alpha-ketoglutarate, ADP, magnesium ions), and ATP transmembrane transport, with related signaling from insulin/IGF stimuli and oxidative stress. Together these suggest a coherent set of mitochondrial transporters and regulators that control energy exchange and redox state.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":5},{"id":"GO:0051881","count":5},{"id":"GO:0015742","count":5},{"id":"GO:0032869","count":5},{"id":"GO:1990314","count":5}]},{"hash":"2103190087662550163","title":"Plant phytochelatin biosynthesis and proteolysis","description":"The strongest signals are phytochelatin biosynthetic process and proteolysis, suggesting a plant-specific metal detox pathway coupled with protein turnover. Other terms point to broader proteostasis and signaling roles, but the dominant theme centers on phytochelatin production and proteolytic regulation in stress responses.","confidence":"Medium","size":10,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046938","count":7},{"id":"GO:1904715","count":7},{"id":"GO:0006508","count":7},{"id":"GO:0043085","count":7},{"id":"GO:0001881","count":1}]},{"hash":"1027066990991370837","title":"Arginine and Histone Methylation","description":"The top GO terms include clear methylation signals: peptidyl-arginine methylation (asymmetric dimethylarginine) and histone H4-R3 methylation, suggesting a theme around methylation-related regulation, possibly chromatin-associated. However, several other terms are unrelated metabolic processes (nitrate assimilation, cobalamin biosynthesis, cholesterol biosynthesis, phenylacetate catabolism) and general growth/senescence, indicating a mixed set with only a weak overarching theme beyond methylation. This makes the label tentative.","confidence":"Low","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0019919","count":2},{"id":"GO:0043985","count":2}]},{"hash":"950318239311272520","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061158","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0045019","count":2},{"id":"GO:0043066","count":2},{"id":"GO:1903629","count":2}]},{"hash":"251578949148497730","title":"Ion Homeostasis and Membrane Potential","description":"This cluster is dominated by GO terms related to ion regulation and membrane potential, notably intracellular potassium ion homeostasis, regulation of resting membrane potential, and membrane repolarization in cardiac cells, which point to a core function in maintaining ion gradients and electrical activity across membranes. There are additional transport-related terms suggesting membrane-associated export/import activities, but the strongest signals center on ion homeostasis and membrane potential regulation. ","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030007","count":2},{"id":"GO:0060075","count":2},{"id":"GO:0098914","count":2},{"id":"GO:0046618","count":1},{"id":"GO:0006289","count":1}]},{"hash":"1932423250415635881","title":"Unknown","description":"Unknown","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000637","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0061158","count":1},{"id":"GO:0010875","count":1}]},{"hash":"1579896192510367992","title":"Neuronal excitability and mechanosensation","description":"This cluster centers on ion channel regulation and membrane potential changes (potassium channels, membrane hyperpolarization, potassium export) along with mechanosensory detection (pain and touch). While there is a stray term about stress fibers, the dominant theme is neuronal signaling and mechanosensory responsiveness, suggesting a functional group tied to excitability and mechanosensation.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":1},{"id":"GO:1900454","count":1},{"id":"GO:0071286","count":1},{"id":"GO:0060081","count":1},{"id":"GO:1902260","count":1}]},{"hash":"1940187828513476192","title":"Mitochondrial Energy Metabolism and Transport","description":"This cluster centers on mitochondrial function: transport of metabolites (alpha-ketoglutarate, ADP), ATP translocation, and regulation of membrane potential/permeability, with links to insulin/IGF signaling, fatty acid response, and oxidative stress, pointing to a mitochondrial energy metabolism and signaling theme.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070542","count":2},{"id":"GO:0046902","count":1},{"id":"GO:0051881","count":1},{"id":"GO:0015742","count":1},{"id":"GO:0032869","count":1}]},{"hash":"1998412903135234119","title":"Plant Hormone Signaling and Chromatin Remodeling","description":"The cluster shows a strong emphasis on plant hormone signaling (cytokinin-activated signaling, gibberellin response) together with regulators of gene expression (chromatin remodeling, DNA-templated transcription, snRNA transcription). This suggests a coordinated module linking hormone signaling to transcriptional regulation. Some terms (sporulation, viral process) are more incidental noise and do not overpower the core theme. ","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0009736","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0030435","count":2},{"id":"GO:0009739","count":1}]},{"hash":"1549954603028549336","title":"Unknown","description":"The top GO terms span hypoxia response, fibrinolysis, blood coagulation, development, behavior, and even cellulose catabolic process, which do not converge on a single clear function; the presence of an outlier term (cellulose catabolic process) suggests annotation noise, so a cohesive, specific label cannot be assigned.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001666","count":2},{"id":"GO:0030245","count":2},{"id":"GO:0042730","count":2},{"id":"GO:0051918","count":2},{"id":"GO:0007596","count":2}]},{"hash":"829182812617162610","title":"Steroid and lipid metabolism and transport","description":"This cluster is dominated by GO terms tied to lipid and steroid metabolism and transport: progesterone biosynthetic process, intracellular cholesterol transport, bile acid secretion, ceramide transport, and PPAR signaling; plus glucocorticoid metabolism and growth hormone response, which reflect lipid-hormone signaling. Some developmental terms (heart morphogenesis, integument development) suggest these lipid pathways may also influence development. The dataset shows a cohesive lipid/hormone theme despite sparse connections, supporting this label.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080060","count":1},{"id":"GO:0035621","count":1},{"id":"GO:0006701","count":1},{"id":"GO:0035360","count":1},{"id":"GO:0032782","count":1}]},{"hash":"707681081090994788","title":"Unknown","description":"There is no single shared function linking these GO terms: RNA processing (snoRNP assembly), LDL receptor\u2013related lipid receptor trafficking/catabolic processes, sporulation, pheromone maturation, and embryonic development terms are scattered across different biological contexts, so a cohesive, representative cluster label cannot be determined.","confidence":"","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000492","count":1},{"id":"GO:1905596","count":1},{"id":"GO:0030435","count":1},{"id":"GO:0090472","count":1},{"id":"GO:0007354","count":1}]},{"hash":"2104070851435963866","title":"Biosynthesis and RNA Methylation Enzymes","description":"The GO terms show multiple biosynthetic pathways (cobalamin, biotin, polyamine, vitamin E, phosphatidylcholine) alongside RNA methylation and modification activities (m7G capping, guanine-N7 methylation, rRNA modification, histone methylation). This points to a set of proteins involved in diverse biosynthetic processes as well as nucleic acid modification, rather than a single pathway. The lack of edges suggests annotation-based grouping rather than direct interactions, so a label that combines biosynthesis and methylation functions fits well.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":2},{"id":"GO:0006370","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0009102","count":1},{"id":"GO:0006596","count":1}]},{"hash":"2039451367291602239","title":"Membrane Transporters and Oligomerization","description":"The cluster\u2019s terms cluster around transmembrane transport of diverse substrates (nitrite, nitrate, phosphate, sodium, galactose, fucose, vitamin) and a note on protein homooligomerization, suggesting transporter subunits forming membrane channels or complexes; the neurotransmitter loading term aligns with vesicle-associated transport, reinforcing a transporter/vesicle activity theme.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0015707","count":1},{"id":"GO:0035435","count":1},{"id":"GO:0015706","count":1},{"id":"GO:0006004","count":1}]},{"hash":"1806973747970821844","title":"ER stress response and ubiquitin-mediated degradation","description":"The GO terms highlight unfolded protein response and proteostasis-related processes (response to unfolded protein, K11-linked ubiquitination), pointing to ER-associated protein quality control and targeted degradation. Although a few terms are obsolete, the dominant theme is protein folding stress and ubiquitin-dependent degradation, with a secondary hint of stress-related signaling.","confidence":"High","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051348","count":1},{"id":"GO:0016576","count":1},{"id":"GO:1903071","count":1},{"id":"GO:0043278","count":1},{"id":"GO:0006986","count":1}]},{"hash":"1607804486154654443","title":"Ubiquinone biosynthesis and lipid homeostasis","description":"This cluster is enriched for terms related to ubiquinone (coenzyme Q) biosynthesis and lipid homeostasis, including regulation of ubiquinone biosynthetic process and tocopherol cyclase activity, with supporting lipid metabolism terms. Some terms are obsolete or unrelated (Purkinje cell layer morphogenesis), but the core theme ties to CoQ production and lipid regulation.","confidence":"Medium","size":10,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":1},{"id":"GO:0019509","count":1},{"id":"GO:1901006","count":1},{"id":"GO:0055088","count":1},{"id":"GO:0010795","count":1}]},{"hash":"1894967030370403352","title":"Ubiquitin-Proteasome System and Wnt/NF-\u03baB Signaling","description":"The top GO terms point to ubiquitin-dependent proteolysis via SCF and proteasomes, along with deubiquitination, indicating a core role in protein turnover. The simultaneous representation of canonical/non-canonical Wnt signaling regulation and NF-\u03baB signaling suggests these proteins also modulate key signaling pathways, potentially linking proteostasis to pathway control. Some terms (virus-related, inflammatory regulation) may reflect broader immune signaling connections, but the dominant theme remains ubiquitin-proteasome\u2013mediated regulation with signaling cross-talk.","confidence":"High","size":9,"edges":3,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0038061","count":2},{"id":"GO:0090263","count":2},{"id":"GO:0090090","count":2},{"id":"GO:0010043","count":2}]},{"hash":"2005456722894571613","title":"Ribosome Assembly and Translation","description":"The top terms are dominated by translation (GO:0006412, 2 proteins) and ribosomal small subunit assembly (GO:0000028, 1), indicating a core link to protein synthesis machinery. Other terms are singletons and span unrelated processes (ubiquitination, DNA repair, spindle pole body duplication), suggesting incidental annotations. Therefore, this cluster most representatively reflects ribosome biogenesis and translation.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0010637","count":1},{"id":"GO:1904378","count":1},{"id":"GO:1901340","count":1},{"id":"GO:0014070","count":1}]},{"hash":"1039764365844594982","title":"Lipid metabolism and vesicle transport","description":"The top GO terms cluster around lipid biosynthesis and turnover (mevalonate/isoprenoid pathway, sphingomyelin catabolic process, lipid A biosynthetic process) and ER-to-Golgi vesicle transport, suggesting a theme of lipid metabolism linked to membrane trafficking. Some terms (vascular branching, cardiac hypertrophy) are tissue-specific or obsolete and may reflect broader signaling contexts or annotation noise.","confidence":"Medium","size":9,"edges":33,"triangles":64,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001569","count":9},{"id":"GO:0016576","count":9},{"id":"GO:0035690","count":9},{"id":"GO:1900486","count":9},{"id":"GO:0006685","count":9}]},{"hash":"100184103165288356","title":"Chromatin regulation and histone modification","description":"The GO terms cluster around chromatin state control and transcriptional regulation, including regulation of transcription start site selection, histone acetylation and ubiquitination, heterochromatin formation, and nucleosome dynamics. Although several terms are obsolete, they point to a cohesive theme of chromatin remodeling and epigenetic regulation.","confidence":"Medium","size":9,"edges":36,"triangles":84,"max_degree":8,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071441","count":6},{"id":"GO:0001178","count":6},{"id":"GO:0030491","count":6},{"id":"GO:0042766","count":6},{"id":"GO:0071894","count":6}]},{"hash":"1168864939770458724","title":"Unknown","description":"The GO terms are spread across diverse cellular processes (mitochondrial fusion regulation, ERAD-related maintenance, calcium channel regulation, spindle pole body duplication, erythrocyte differentiation, ubiquitination, ribosome assembly, nucleotide-excision repair, and autophagosome maturation) with little overlap. The presence of obsolete terms and no clear shared pathway makes it unclear how these proteins function together, so I label this cluster Unknown.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010637","count":1},{"id":"GO:1904378","count":1},{"id":"GO:1901340","count":1},{"id":"GO:0014070","count":1},{"id":"GO:0030474","count":1}]},{"hash":"1994527332605412731","title":"Cell cycle control and ubiquitin-proteasome degradation","description":"The cluster centers on G1/S and G2/M mitotic transitions and ubiquitin-dependent proteolysis (including SCF-mediated degradation), pointing to coordinated regulation of cell cycle progression via targeted protein turnover. While some terms touch on hematopoiesis and morphogenesis, the dominant theme is cell cycle control through ubiquitin-mediated degradation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000086","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0000082","count":2},{"id":"GO:0030097","count":2},{"id":"GO:0030433","count":2}]},{"hash":"361479389485251243","title":"Septin Ring Assembly and Cytokinesis","description":"The top GO terms are dominated by septin ring formation and division processes (division septum, septin ring assembly, bud neck organization, cytokinesis, and spindle assembly), pointing to a septin-driven cell division role, likely in budding yeasts, with a minor presence of general cell division and meiosis-related terms. ER folding and calcium export appear but are not central to the cluster\u2019s main theme.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034975","count":2},{"id":"GO:1990034","count":2},{"id":"GO:0000917","count":1},{"id":"GO:0007056","count":1},{"id":"GO:0032186","count":1}]},{"hash":"1357949211735814441","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":15,"triangles":12,"max_degree":6,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0000398","count":6},{"id":"GO:0048701","count":6},{"id":"GO:0000462","count":5},{"id":"GO:1990417","count":4}]},{"hash":"238295995447087430","title":"Ubiquitin-mediated signaling and apoptosis","description":"The top GO terms point to ubiquitin-related regulation (K63-linked ubiquitination, ubiquitin-dependent proteolysis, autoubiquitination) and modulation of signaling pathways (JNK regulation, TGF-\u03b2 receptor signaling), together with processes like apoptosis and ribophagy. This suggests the proteins function together in ubiquitin-dependent control of signaling and cell fate, including autophagy-related turnover and programmed cell death.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030512","count":5},{"id":"GO:0046328","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0060669","count":5},{"id":"GO:0045944","count":5}]},{"hash":"44706948696968644","title":"Histone ubiquitination and NF-\u03baB\u2013apoptosis regulation","description":"The cluster centers on ubiquitin-related processes affecting chromatin (histone ubiquitination/catabolism, autoubiquitination) and links to signaling pathways that control cell survival and growth (NF-\u03baB activation, apoptosis regulation). There are competitive notes about Wnt receptor turnover and chromatin-level regulation (dosage compensation), supporting a cohesive theme of ubiquitin-mediated chromatin regulation interfacing with NF-\u03baB and apoptotic signaling.","confidence":"Medium","size":9,"edges":4,"triangles":1,"max_degree":3,"top_function":"autophagy","top_go_terms":[{"id":"GO:0070535","count":6},{"id":"GO:0036205","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0090073","count":4},{"id":"GO:1903721","count":4}]},{"hash":"1956356956586310700","title":"Ubiquitin-dependent proteostasis and stress signaling","description":"Top GO terms cluster around ubiquitination processes (autoubiquitination, K63-linked ubiquitination, ubiquitin-dependent degradation pathways) and chaperone-mediated assembly, with additional links to cellular stress responses (ethanol, chitin, glucocorticoid metabolism). This suggests a coherent role in tagging and processing misfolded or regulatory proteins and coordinating proteostasis with stress signaling.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090035","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0070534","count":4},{"id":"GO:0071361","count":4},{"id":"GO:0030579","count":4}]},{"hash":"1416043671645009952","title":"Nucleotide Biosynthesis and Salvage","description":"The cluster is driven by GO terms related to nucleotide metabolism, including ADP biosynthetic process, AMP salvage, CDP biosynthetic process, nucleoside monophosphate phosphorylation, and purine ribonucleotide interconversion, indicating a cohesive focus on nucleotide production and interconversion. Some development-related terms (brain and liver development) appear but are secondary to the central nucleotide metabolism theme. Confidence in this label reflecting the cluster\u2019s primary function is High.","confidence":"High","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":3},{"id":"GO:0042493","count":3},{"id":"GO:0046939","count":2},{"id":"GO:0046041","count":2},{"id":"GO:0006172","count":2}]},{"hash":"134834270436984932","title":"Ubiquitin-Mediated Regulation and Degradation","description":"These proteins show strong enrichment for ubiquitin-related processes (autoubiquitination, polyubiquitination, ERAD) and regulation of growth-related signaling, including negative regulation of transcription, apoptosis, organ growth, and Wnt receptor turnover. The combination suggests a cohesive role in ubiquitin-driven control of signaling, protein turnover, and cell fate, with some peripheral links to ubiquitin-modulated pathways like TLR signaling and peroxisomal protein import.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0000122","count":4},{"id":"GO:0043066","count":4},{"id":"GO:0038018","count":4},{"id":"GO:0046621","count":4}]},{"hash":"1721025692015795509","title":"Lipid metabolism and ER-Golgi transport","description":"The cluster\u2019s recurring GO terms cluster around lipid-related processes (mevalonate/isoprenoid biosynthesis, sphingomyelin catabolism, lipid A biosynthesis) and membrane trafficking (ER to Golgi vesicle transport). While a few terms are peripheral or obsolete, the lipid metabolism and vesicle transport themes are the most coherent across the set, supporting a lipid/metabolism-transport cluster label.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0001569","count":2},{"id":"GO:0016576","count":2},{"id":"GO:0035690","count":2},{"id":"GO:1900486","count":2},{"id":"GO:0006685","count":2}]},{"hash":"2087520436883569860","title":"Nuclear transcription regulation and RNA processing","description":"These proteins appear to participate in nuclear control of gene expression and RNA processing. The top GO terms point to transcription start site regulation by RNA polymerase II, regulation of mRNA splicing, and ncRNA-mediated gene silencing, alongside chromatin-related activities such as histone acetylation and DNA methylation. Additional signals involve nuclear RNA processing and nucleosome dynamics, suggesting a cohesive role in coordinating transcription with RNA maturation and chromatin state. A minority of terms reference cytoplasmic stress granule localization, which may reflect related RNA handling rather than a primary function of the cluster.","confidence":"Medium","size":9,"edges":34,"triangles":70,"max_degree":8,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0009432","count":6},{"id":"GO:0031047","count":5},{"id":"GO:0048026","count":5},{"id":"GO:0071441","count":4},{"id":"GO:0001178","count":4}]},{"hash":"312889219899782778","title":"Redox Homeostasis and Mitochondrial Regulation","description":"The proteins show enrichment for oxidative detoxification and glutathione metabolism, plus regulation of mitochondrial membrane potential, pointing to a shared role in managing oxidative stress and mitochondrial function. Some terms touch on CNS-related processes (oligodendrocyte development) or ethanol response, but the dominant signal is redox balance and mitochondrial regulation.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":4},{"id":"GO:0014003","count":3},{"id":"GO:0045471","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0070527","count":2}]},{"hash":"367787962380648728","title":"Nuclear DNA replication and chromatin regulation","description":"The terms cluster around core nuclear processes: DNA replication is prominent, with supporting signals for chromatin modification regulation (histone acetylation) and transcription start site control, plus RNA processing events (snoRNA release, rRNA catabolic process) in the nucleus. This suggests a cohesive theme of genome maintenance and ribosome-related RNA processing within the nucleus, despite some development or obsolete annotations.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0048701","count":4},{"id":"GO:0071441","count":3},{"id":"GO:0001178","count":3},{"id":"GO:1990417","count":3}]},{"hash":"831295540073010787","title":"Unknown","description":"The top GO terms span embryonic development, reproductive processes, and DNA repair, but also xenobiotic export, peroxisomal fatty acid import, and bacterial teichoic acid and bacteriocin transport/immunity. This mix across eukaryotic development, metabolism, and prokaryotic transport suggests no single cohesive function for the cluster, making a specific, representative label inappropriate.","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008283","count":3},{"id":"GO:0001701","count":3},{"id":"GO:0006289","count":3},{"id":"GO:0048240","count":3},{"id":"GO:0040016","count":2}]},{"hash":"1007637523368336315","title":"Unknown","description":"The Top Terms are highly diverse, including viral process, DNA-templated transcription, various biosynthetic and metabolic processes, tRNA modification, protein methylation, ER stress response, and cell cycle regulation. There is no clear, single functional theme tying these proteins together, and the lack of edges supports assigning a generic,Unknown label rather than a specific biological function.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016032","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0090266","count":1},{"id":"GO:0010906","count":1},{"id":"GO:1901106","count":1}]},{"hash":"2124155740859903782","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060271","count":9},{"id":"GO:0050709","count":9},{"id":"GO:0006547","count":9},{"id":"GO:0007117","count":9},{"id":"GO:0051301","count":9}]},{"hash":"1323174949864922761","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":14,"triangles":0,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0036205","count":1},{"id":"GO:0048536","count":1},{"id":"GO:0061158","count":1},{"id":"GO:0097039","count":1},{"id":"GO:0051865","count":1}]},{"hash":"2154430997998566378","title":"Plant immune signaling and RNA regulation","description":"The Top Terms point to plant-specific defense processes (positive regulation of plant-type hypersensitive response) alongside RNA-level control (regulation of mRNA stability, polyadenylation, and translation initiation) and ROS management (removal of superoxide radicals, response to oxidative stress). Together, these suggest a cluster of proteins involved in coordinating transcriptional/post-transcriptional responses during plant immune signaling and oxidative stress, with some terms reflecting virus\u2013host interactions. ","confidence":"Medium","size":9,"edges":33,"triangles":65,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:1900363","count":2},{"id":"GO:0043488","count":1},{"id":"GO:0034052","count":1},{"id":"GO:1903679","count":1},{"id":"GO:0044829","count":1}]},{"hash":"285521703772859539","title":"Ribosome Biogenesis and rRNA Processing","description":"The cluster's top GO terms are dominated by ribosome biogenesis, large subunit biogenesis and export, as well as rRNA processing steps, suggesting the proteins mostly function in ribosome assembly and maturation. A few terms (mitotic chromosome alignment, hematopoietic differentiation) are less clearly connected and may reflect broader or indirect annotations, but the ribosome-related terms provide a coherent core function.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018401","count":1},{"id":"GO:0055114","count":1},{"id":"GO:1901874","count":1},{"id":"GO:0032364","count":1},{"id":"GO:0042254","count":1}]},{"hash":"476316129402233174","title":"Mitochondrial transport and membrane potential regulation","description":"The cluster centers on mitochondrial inner-mmembrane transport (ATP/ADP, alpha-ketoglutarate, magnesium ions) and regulation of membrane permeability/potential, plus a reactive oxygen species response. These terms together indicate a cohesive module of mitochondrial energy metabolism and ion transport, with insulin/IGF signaling suggesting metabolic regulation rather than a separate pathway. Therefore, the name captures the core shared function of these proteins.","confidence":"High","size":9,"edges":17,"triangles":15,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":1},{"id":"GO:0051881","count":1},{"id":"GO:0015742","count":1},{"id":"GO:0032869","count":1},{"id":"GO:1990314","count":1}]},{"hash":"1134165613972901048","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006398","count":1},{"id":"GO:0033260","count":1},{"id":"GO:0030961","count":1},{"id":"GO:0034720","count":1},{"id":"GO:0070544","count":1}]},{"hash":"806877285310050091","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":2},{"id":"GO:0000472","count":2},{"id":"GO:0006368","count":2},{"id":"GO:0071039","count":1},{"id":"GO:0071035","count":1}]},{"hash":"2222151478586380084","title":"Developmental differentiation and signaling","description":"The cluster's GO terms center on tissue differentiation (lung epithelium) and morphogenesis (blood vessel branching), along with broad signaling processes (GTPase activity, transcription regulation, cytokinesis), suggesting a theme of developmental differentiation and associated signaling networks across tissues. Some terms are general or neuronal (LTP), but overall the signals point to developmental regulation and cell signaling. ","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060487","count":4},{"id":"GO:0045944","count":4},{"id":"GO:0006469","count":4},{"id":"GO:0032465","count":4},{"id":"GO:0043547","count":4}]},{"hash":"61367303566856663","title":"Vertebrate Developmental Genes","description":"The top GO terms show strong emphasis on neural tube closure, forebrain development, skeletal system development, and multicellular organism development, which together indicate proteins involved in vertebrate development. A few terms reflect stress responses or immune signaling, but they are less central to the cluster. Therefore the label captures the dominant theme of developmental function among the proteins.","confidence":"High","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001843","count":7},{"id":"GO:0050830","count":7},{"id":"GO:0001403","count":7},{"id":"GO:0000278","count":7},{"id":"GO:0001501","count":7}]},{"hash":"1193075846154507786","title":"B cell antibody diversification and DNA repair","description":"The GO terms point to B-cell\u2013specific processes like somatic hypermutation, isotype switching, memory, and humoral immune response, alongside general DNA repair and genome maintenance (base/excision repair, nucleotide excision repair, DNA replication, and mitotic checkpoint regulation). This suggests a cluster of proteins engaged in antibody diversification coupled with DNA repair and genome stability during B cell maturation.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045876","count":1},{"id":"GO:0045190","count":1},{"id":"GO:0006286","count":1},{"id":"GO:0007613","count":1},{"id":"GO:0002455","count":1}]},{"hash":"2268488126621729691","title":"Membrane Solute Transporters","description":"The top GO terms indicate transmembrane transport of diverse solutes (sodium, nitrate, arabinose, glucose, urate, trehalose, dehydroascorbic acid), suggesting a cohesive cluster of membrane transport proteins; a couple of terms on translation and seedling development appear as outliers.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":2},{"id":"GO:0006412","count":1},{"id":"GO:0090351","count":1},{"id":"GO:0015706","count":1},{"id":"GO:1904728","count":1}]},{"hash":"818651888978505992","title":"RNA processing and translational control","description":"This cluster centers on RNA metabolism and translation-related functions: splicing regulation, mRNA modification, RNA silencing, and components involved in ribosome biogenesis and translation initiation. The presence of chloroplast organization and development-related terms may reflect multifunctional proteins or broad annotations, but the dominant signal is post-transcriptional gene regulation and protein synthesis.","confidence":"Medium","size":9,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0032147","count":1},{"id":"GO:0000381","count":1},{"id":"GO:0016556","count":1},{"id":"GO:0009658","count":1}]},{"hash":"368942814132958191","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0033129","count":2},{"id":"GO:0070935","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0060044","count":2},{"id":"GO:0030216","count":2}]},{"hash":"657543128289301073","title":"Toll-like Receptor Signaling and Cytokine Production","description":"The terms are dominated by Toll-like receptor signaling (TLR8/9/10) and the broader Toll pathway, along with cytokine and interferon production, pointing to a coherent innate immune signaling module activated by fungal cues. Some outliers (dopamine response, kidney size) are peripheral, but the core theme is TLR-driven immune sensing and cytokine regulation.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0009620","count":3},{"id":"GO:0034162","count":3},{"id":"GO:1902499","count":3},{"id":"GO:1903351","count":3},{"id":"GO:0034158","count":3}]},{"hash":"1754516551258755814","title":"mRNA Splicing and Translation Initiation","description":"These proteins show strong ties to splicing-related processes (regulation of alternative mRNA splicing via spliceosome, splice site recognition, small-subunit processome assembly) and to translation initiation (preinitiation complex formation, eIF4F complex assembly), along with mRNA modification and stabilization. The cluster therefore centers on RNA processing coupled with initiation/regulation of translation, justifying this label.","confidence":"High","size":9,"edges":5,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0016556","count":2},{"id":"GO:0001825","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0035278","count":2}]},{"hash":"23710614751233796","title":"Ribosome biogenesis and translation fidelity","description":"The cluster is dominated by translation- and ribosome-related terms (translation, ribosome biogenesis, maintenance of translational fidelity) and rRNA modification (pseudouridine synthesis), indicating a cohesive theme around ribosome assembly and accurate protein synthesis. Although a few transcription termination/antitermination and stress-related terms appear, the strongest signal centers on ribosome production and fidelity control, with some antibiotic and heat stress associations as secondary references.","confidence":"High","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0006412","count":7},{"id":"GO:0042254","count":4},{"id":"GO:0046677","count":3},{"id":"GO:0045903","count":2},{"id":"GO:0000455","count":2}]},{"hash":"1907855821776797365","title":"Proteostasis and Unfolded Protein Response","description":"The cluster is dominated by proteostasis-related terms: protein folding in the ER, response to unfolded protein, and nuclear protein quality control by the ubiquitin-proteasome system, plus a heat-response connection. These point to a cohesive theme of managing misfolded proteins and maintaining protein homeostasis under stress. A few terms (DNA replication, a developmental signaling term) are less related and may be noise, but do not override the central proteostasis signal.","confidence":"High","size":9,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":1},{"id":"GO:0006260","count":1},{"id":"GO:1900035","count":1},{"id":"GO:1901621","count":1},{"id":"GO:0034975","count":1}]},{"hash":"1894566578758915190","title":"DNA Replication and Repair","description":"This cluster is dominated by GO terms for DNA replication, mitotic DNA replication checkpoint signaling, UV-damage excision repair, and translesion synthesis, pointing to genome maintenance as the core function; additional terms for protein oligomerization/assembly suggest the involvement of multi-subunit complexes, with a few peroxisome/mitochondrial assembly annotations likely incidental.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001824","count":4},{"id":"GO:0051260","count":3},{"id":"GO:0016562","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0034214","count":3}]},{"hash":"837145511537103494","title":"Biosynthesis and protein complex assembly","description":"Top GO terms point to metabolic biosynthesis (cholesterol, thiamine, carbohydrate phosphorylation) alongside protein multimerization and assembly (homooligomerization, hexamerization, complex III assembly, peroxisomal import). The combination suggests a theme around producing biomolecules and assembling protein complexes, with a few outliers (DNA replication, peroxisomal transport). The single-edge connectivity indicates a loose association, but the shared emphasis on biosynthetic and assembly processes supports this label.","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0051260","count":1},{"id":"GO:0016562","count":1}]},{"hash":"1779978256159725695","title":"Fatty acid biosynthesis and central metabolism","description":"The cluster shows strong signals for fatty acid biosynthetic processes across chain lengths, plus pathways feeding into energy metabolism (pyruvate decarboxylation to acetyl-CoA and the TCA cycle) and even menaquinone biosynthesis, with peroxisomal protein import/recycling suggesting lipid-handling roles. Antibiotic biosynthesis is present but less dominant, so the core theme is fatty acid production and central carbon metabolism.","confidence":"High","size":9,"edges":21,"triangles":30,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0019367","count":2},{"id":"GO:0051790","count":2},{"id":"GO:0051792","count":2},{"id":"GO:0006633","count":2}]},{"hash":"106750860917846578","title":"DNA replication and repair proteins","description":"Most terms point to DNA replication and DNA damage response pathways, including DNA replication, mitotic DNA replication checkpoint signaling, UV-damage excision repair, and error-free translesion synthesis. Some terms about protein oligomerization/hexamerization likely reflect assembly of replication or repair complexes. A few organelle import/assembly terms are less clearly related and may be annotation noise. Overall, the cluster is dominated by genome maintenance activities.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0016562","count":3},{"id":"GO:0006260","count":3},{"id":"GO:0034214","count":3},{"id":"GO:0034551","count":3}]},{"hash":"766769392499741761","title":"Developmental Signaling and Cellular Stress Responses","description":"The top GO terms span developmental processes (lung mesenchyme and corpus callosum development), broad signaling (potassium transport, B cell receptor signaling), and stress responses (apoptosis regulation, cellular responses to amino acid starvation and virus). This suggests the proteins act as regulators across development and various cellular stress and signaling pathways, rather than a single, cohesive function. ","confidence":"Medium","size":9,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006813","count":7},{"id":"GO:0016477","count":6},{"id":"GO:0010898","count":6},{"id":"GO:0060484","count":6},{"id":"GO:0022038","count":6}]},{"hash":"1317752877815688903","title":"Unknown","description":"The top terms include neural tube closure, corpus callosum development, and trachea formation (developmental morphogenesis), but also terms for immune signaling, biofilm formation, and responses to virus and starvation. This mix suggests there is no single, cohesive function dominating the cluster, so a concise, representative label cannot be determined.","confidence":"","size":9,"edges":33,"triangles":64,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016477","count":9},{"id":"GO:0010898","count":9},{"id":"GO:0022038","count":9},{"id":"GO:0050853","count":9},{"id":"GO:0043065","count":9}]},{"hash":"1220108628594778467","title":"Bacterial core biosynthesis and division","description":"The Top Terms span diverse but fundamental bacterial processes: cobalamin biosynthesis, tRNA wobble uridine modification, and various polysaccharide and lipopolysaccharide biosyntheses (envelope components), along with iron-sulfur cluster assembly, plasmid partitioning, chromosome segregation, and cell cycle. This suggests a cluster of proteins involved in essential, broad housekeeping functions\u2014biosynthesis, genome maintenance, and basic cell growth\u2014rather than a single specific pathway. The sparse connectivity (one edge, no triangles) further supports a loose grouping by general cellular essentiality. ","confidence":"Medium","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":3},{"id":"GO:0002098","count":2},{"id":"GO:0006859","count":1},{"id":"GO:0009103","count":1},{"id":"GO:0045226","count":1}]},{"hash":"1901778042927548837","title":"Mitochondrial metabolism and hematopoiesis","description":"This cluster shows enrichment for mitochondrial electron transport (NADH to ubiquinone) and cofactor metabolism (thiamine, tetrahydrofolate), along with regulation of erythrocyte and megakaryocyte differentiation. Despite some obsolete GO terms, the core signal links energy metabolism to hematopoietic cell development.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":9},{"id":"GO:0009228","count":8},{"id":"GO:0046653","count":8},{"id":"GO:0010725","count":8},{"id":"GO:0014063","count":8}]},{"hash":"780547795160577982","title":"ER-Golgi trafficking and Golgi localization","description":"The top GO terms point to a cohesive secretory pathway theme, dominated by ER-to-Golgi vesicle transport, COPII vesicle budding, retrograde Golgi\u2013ER transport, and protein localization to the Golgi. Although cell division and brain development terms appear, the recurring emphasis on vesicle trafficking and Golgi localization suggests the proteins function primarily in the ER-Golgi transport pathway and Golgi targeting.","confidence":"High","size":9,"edges":18,"triangles":14,"max_degree":8,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006888","count":7},{"id":"GO:0090307","count":7},{"id":"GO:0035264","count":7},{"id":"GO:0008283","count":7},{"id":"GO:0006890","count":7}]},{"hash":"726989210666252836","title":"ER protein folding and heat stress response","description":"This cluster is dominated by terms related to protein folding in the endoplasmic reticulum, unfolded protein response, and heat-stress response, pointing to proteostasis and stress handling in the secretory pathway. While a few terms hint at developmental signaling and translation regulation, the strongest thread links ER-associated folding and cellular stress responses. ","confidence":"Medium","size":9,"edges":34,"triangles":71,"max_degree":8,"top_function":null,"top_go_terms":[{"id":"GO:0006469","count":2},{"id":"GO:0001569","count":2},{"id":"GO:0009408","count":1},{"id":"GO:0006260","count":1},{"id":"GO:1900035","count":1}]},{"hash":"1395084038871891560","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0001731","count":3},{"id":"GO:0002188","count":3}]},{"hash":"1846759704597425146","title":"Mitochondrial Transport and Energy Regulation","description":"The top GO terms cluster around mitochondrial membrane transport (ADP/ATP, alpha-ketoglutarate, Mg2+), and regulation of membrane potential/permeability, plus energy-related and redox-related signaling, suggesting a coherent theme of mitochondrial metabolite transport and bioenergetics. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097274","count":7},{"id":"GO:0046902","count":6},{"id":"GO:0051881","count":6},{"id":"GO:0015742","count":6},{"id":"GO:0032869","count":6}]},{"hash":"1571138646798870724","title":"Ubiquitin-Proteasome\u2013Mediated Protein Quality Control","description":"This cluster shows a strong signal for ubiquitination and nuclear protein quality control by the ubiquitin-proteasome system, supported by related terms such as protein ubiquitination and nuclear quality control. Additional hints from chaperone-dependent refolding and other PTMs point to proteostasis and post-translational modification rather than a single signaling pathway.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":2},{"id":"GO:0097284","count":2},{"id":"GO:0006836","count":1},{"id":"GO:2000372","count":1},{"id":"GO:0016567","count":1}]},{"hash":"1698579166074072201","title":"Unknown","description":"The top GO terms include antibiotic/xenobiotic responses alongside several unrelated developmental and cellular processes, with no single cohesive function tying all members together. This lack of a clear shared theme suggests unknown function for the cluster.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0034605","count":1},{"id":"GO:0030655","count":1},{"id":"GO:0019876","count":1},{"id":"GO:0033252","count":1}]},{"hash":"1799240197889464066","title":"Proteostasis and Heat Shock Response","description":"The GO terms cluster around heat response, unfolded protein response, ER protein folding, and ubiquitin-proteasome\u2013mediated quality control, indicating a cohesive proteostasis/quality-control theme under stress. Occasional terms like DNA replication or signaling regulation seem ancillary. The dominant signal is maintenance of protein folding and turnover during heat stress.","confidence":"High","size":9,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1900035","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0034975","count":2}]},{"hash":"1717256343359589541","title":"Calcium signaling in heart development and synaptic plasticity","description":"This cluster combines cardiovascular development signals (heart development and vascular branching) with neural plasticity (long-term synaptic potentiation) and calcium signaling (regulated release of sequestered calcium into the cytosol). The recurring theme is calcium-driven signaling that links heart/circulatory development to synaptic plasticity, with ancillary stress and xenobiotic response associations.","confidence":"High","size":9,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0051412","count":2},{"id":"GO:0001569","count":2},{"id":"GO:1901841","count":2},{"id":"GO:1900271","count":2}]},{"hash":"1424361296219380400","title":"Photosynthesis Light-Response Proteins","description":"The top GO terms cluster around responses to various light conditions (blue, red, UV-A; high/low light), photosynthesis, light harvesting, and nonphotochemical quenching, indicating involvement in light capture and photoprotection of photosystems. The presence of phytol/chlorophyll-related terms also points to chlorophyll biosynthesis aspects linked to photosynthetic capacity. Overall, these proteins appear to participate in photosynthetic light sensing and utilization.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071486","count":1},{"id":"GO:0009645","count":1},{"id":"GO:0018298","count":1},{"id":"GO:1904964","count":1},{"id":"GO:0010114","count":1}]},{"hash":"491826364139070283","title":"Unknown","description":"The GO terms are a highly heterogeneous mix (metabolic cofactor biosynthesis like glutathione, thiamine, tetrahydrofolate; siderophore ferrichrome; plus unrelated processes such as cell wall organization and erythrocyte differentiation), offering no single cohesive function for the cluster. This makes a clear, representative label difficult to assign.","confidence":"","size":9,"edges":8,"triangles":0,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0046886","count":1},{"id":"GO:0006214","count":1},{"id":"GO:0006749","count":1},{"id":"GO:0045648","count":1}]},{"hash":"61643200561989687","title":"Chromatin organization and transcription regulation","description":"Top terms point to nucleosome assembly, histone modifications (H3-K27 acetylation, H3-K4 dimethylation), and DNA methylation\u2013related chromatin states, along with transcriptional repression. Additional terms touch on spermatid nucleus differentiation and apoptotic signaling, but the core signal is chromatin organization linked to gene expression control. The cluster seems best described as a chromatin-centric group with transcriptional regulation activities.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0090308","count":3},{"id":"GO:0006334","count":3},{"id":"GO:0007098","count":3},{"id":"GO:1901536","count":3},{"id":"GO:0070562","count":3}]},{"hash":"1011704995040294249","title":"Ribosome biogenesis and rRNA maturation","description":"This cluster is enriched for rRNA maturation and ribosomal large subunit biogenesis (SSU/LSU rRNA processing, 5.8S maturation), indicating involvement in ribosome assembly and RNA processing. Additional terms on RNA modification and spliceosome-related processes are present but secondary to the ribosome-focused signals.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000463","count":3},{"id":"GO:0000466","count":3},{"id":"GO:0042273","count":2},{"id":"GO:0000462","count":2},{"id":"GO:0035948","count":2}]},{"hash":"1341109777302059904","title":"Unknown","description":"Unknown","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019619","count":1},{"id":"GO:1905012","count":1},{"id":"GO:0046874","count":1},{"id":"GO:1905004","count":1},{"id":"GO:0070527","count":1}]},{"hash":"152640170053133419","title":"Unknown","description":"The GO terms are scattered across diverse areas: angiogenesis, xenobiotic response, lipid metabolism (mevalonate/IPP, sphingomyelin, lipid A), vesicle transport between ER and Golgi, and some obsolete annotations, with no single cohesive process tying them together. There isn\u2019t a clear, representative theme for a concise label.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001569","count":2},{"id":"GO:0016576","count":2},{"id":"GO:0035690","count":2},{"id":"GO:1900486","count":2},{"id":"GO:0006685","count":2}]},{"hash":"252070920316447319","title":"ER Retention and Retrograde Trafficking","description":"Top GO terms indicate ER retention and retrograde trafficking (ER to cytosol), ER-associated degradation, and Golgi-related transport, with a touch of lysosome organization. Together they define a small module of ER quality control and intracellular trafficking rather than a soluble metabolic function.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006621","count":1},{"id":"GO:0030433","count":1},{"id":"GO:1904153","count":1},{"id":"GO:0030970","count":1},{"id":"GO:0046909","count":1}]},{"hash":"1314592615882540215","title":"Cellular stress response and translational control","description":"Top GO terms point to responses to multiple stressors (acidic pH, hydrogen peroxide, UV-C) and to stress-related transcriptional and translational regulation (GCN2 signaling, positive regulation of translational initiation in response to starvation). This suggests a functional cluster of proteins involved in sensing and responding to cellular stress and adjusting protein synthesis accordingly. A few terms like neuron projection extension or negative regulation of protein-containing complex assembly are less central but can appear in signaling networks that cross-talk with stress pathways.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031953","count":1},{"id":"GO:1990138","count":1},{"id":"GO:0071468","count":1},{"id":"GO:0097201","count":1},{"id":"GO:0031333","count":1}]},{"hash":"1913746966173015868","title":"Embryonic Development and Tissue Differentiation","description":"The top GO terms point to development and differentiation across multiple tissues and organs (e.g., endocardial cushion and left/right patterning, cartilage morphogenesis, endocrine system development, placental/embryonic tissue differentiation, pancreatic cell development). Some terms are outliers (plant-related responses, DNA repair), but the main signal is embryonic development and lineage specification.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003198","count":1},{"id":"GO:0060972","count":1},{"id":"GO:0035270","count":1},{"id":"GO:0060536","count":1},{"id":"GO:0060707","count":1}]},{"hash":"715726297816996501","title":"Neural development and axon guidance","description":"The terms are dominated by nervous system development and axon-guidance processes (facial/acoustic ganglion development, facial nerve organization, retinal ganglion cell axon guidance, cerebellar Purkinje cell development, neuronal migration). A few terms mention angiogenesis or fertilization, which may be incidental associations, but the core theme centers on neural development and axon pathfinding.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903375","count":1},{"id":"GO:0060978","count":1},{"id":"GO:0048903","count":1},{"id":"GO:0021828","count":1},{"id":"GO:1902336","count":1}]},{"hash":"557294565621862919","title":"Steroid and lipid biosynthesis","description":"The GO terms show a clear emphasis on steroid hormone metabolism (androgen metabolic and catabolic; glucocorticoid biosynthetic) and lipid-related biosynthesis (fatty acid elongation, mycolic acid, melanin biosynthesis), suggesting a cohesive theme around biosynthetic/metabolic processes across different systems. Some terms (lung development, transcription regulation) are less directly aligned, but the dominant signal is biosynthesis and metabolism. ","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008209","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0006710","count":1},{"id":"GO:0030324","count":1},{"id":"GO:0045150","count":1}]},{"hash":"1314160796979559979","title":"Vesicle Trafficking and Golgi Transport","description":"Based on the prominent GO terms related to intracellular membrane trafficking\u2014COPII-coated vesicle cargo loading, retrograde transport from the plasma membrane to the Golgi, recycling endosome to Golgi transport, and regulation of vesicle fusion\u2014the cluster appears to group proteins involved in ER-Golgi and endosomal trafficking. A few terms (apoptosis, immune cell differentiation, ciliogenesis) are peripheral or annotation-noise relative to the central trafficking theme, but the vesicle transport connections are the strongest pattern.","confidence":"High","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033081","count":1},{"id":"GO:0006915","count":1},{"id":"GO:1902543","count":1},{"id":"GO:0035526","count":1},{"id":"GO:1902018","count":1}]},{"hash":"2254385639999973668","title":"Unknown","description":"Unknown because there are no GO terms or network connections to suggest a shared function among the nine proteins; with no enrichment or edges, a meaningful label cannot be assigned.","confidence":"","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"650200241646852722","title":"Plant light-regulated circadian responses","description":"This cluster centers on environmental sensing tied to light and rhythms, especially in plants. Terms include circadian regulation of calcium oscillation, locomotor rhythm, response to absence of light, stomatal movement, and UV protection, which together point to light-driven timing and physiological adjustments. Some terms (magnetoreception, gravitaxis, systemic acquired resistance, meristem regulation) are broader or less directly linked but may reflect overlapping environmental-sensing or plant signaling contexts. Overall, the dominant theme is plant light-responsive and circadian biology.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050958","count":1},{"id":"GO:2000850","count":1},{"id":"GO:0042332","count":1},{"id":"GO:0010617","count":1},{"id":"GO:0045475","count":1}]},{"hash":"675693637007753716","title":"Glycolysis-PPP-Serine Metabolism","description":"The top GO terms cluster around glycolytic process, fructose metabolism, carbohydrate phosphorylation, and serine biosynthesis, with regulatory links to the pentose phosphate pathway (PPP) shunt and flux control toward lactate via pyruvate. This suggests a cohesive theme of central carbon metabolism, including glycolysis, PPP regulation, and serine biosynthesis. A few terms (cobalt ion response, intestinal epithelial cell development) seem less connected and may reflect annotation noise or broader multifunctionality.","confidence":"Medium","size":9,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006000","count":2},{"id":"GO:0046835","count":2},{"id":"GO:0043456","count":2},{"id":"GO:1904024","count":2},{"id":"GO:0006003","count":2}]},{"hash":"2143115415942084880","title":"Telomere/Subtelomeric Heterochromatin Silencing","description":"The cluster is dominated by GO terms for heterochromatin formation and maintenance at subtelomeric and silent mating-type loci, i.e., chromatin silencing in telomeric/subtelomeric domains, with supporting cell-division context.","confidence":"High","size":8,"edges":9,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0006348","count":2},{"id":"GO:0061186","count":2},{"id":"GO:0030466","count":2},{"id":"GO:0006344","count":2}]},{"hash":"243049331184337170","title":"Unknown","description":"The GO terms span diverse systems (immune isotype switching, Rap signaling, neuronal transport, Purkinje cell structure, RNA localization, and cell-cycle transcription regulation) with no single, coherent biological function tying the cluster together, so a clear representative label cannot be assigned.","confidence":"","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045190","count":2},{"id":"GO:0032487","count":2},{"id":"GO:0090419","count":2},{"id":"GO:0033624","count":2},{"id":"GO:0072383","count":2}]},{"hash":"1844277499195535415","title":"Unknown","description":"These eight proteins have a mixed set of GO terms spanning TGF-beta/SMAD signaling, NF-kappaB regulation, plant development, and organelle processes, with no single cohesive theme across all terms. I cannot identify a specific, representative function for the cluster.","confidence":"","size":8,"edges":15,"triangles":14,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030512","count":3},{"id":"GO:0035970","count":3},{"id":"GO:0071560","count":3},{"id":"GO:0046827","count":3},{"id":"GO:0042006","count":3}]},{"hash":"441425362065243044","title":"ER Stress\u2013Induced Ubiquitin-Proteasome Proteostasis","description":"The top GO terms point to ubiquitination, ubiquitin chain formation, and SCF-dependent proteasomal degradation, together with ER-associated degradation and ER-to-cytosol retrograde transport regulation, plus ER-stress\u2013triggered apoptotic signaling. This constellation suggests a cohesive theme of protein quality control in the ER via ubiquitin tagging and proteasomal clearance, with a potential tie to interferon signaling as part of stress responses.","confidence":"High","size":8,"edges":22,"triangles":31,"max_degree":7,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0070059","count":3},{"id":"GO:0010994","count":3},{"id":"GO:1904153","count":3}]},{"hash":"1455196847811421911","title":"Unknown","description":"The top GO terms span immune isotype switching, neural structure, cell cycle regulation, vesicle transport, RNA localization, integrin signaling, and ion channel regulation, with several obsolete terms. There is no single cohesive function that ties these terms together in this cluster, so a specific, representative label cannot be confidently assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045190","count":1},{"id":"GO:0032487","count":1},{"id":"GO:0090419","count":1},{"id":"GO:0033624","count":1},{"id":"GO:0072383","count":1}]},{"hash":"1774071378723542173","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":11,"triangles":5,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":7},{"id":"GO:0048701","count":7},{"id":"GO:1990417","count":4},{"id":"GO:0071035","count":4},{"id":"GO:0014070","count":4}]},{"hash":"878350007842302732","title":"Basement Membrane Remodeling and Morphogenesis","description":"The top GO terms cluster around extracellular matrix remodeling (basement membrane disassembly, collagen catabolic process) and epithelial morphogenesis (lung tube branching), indicating a shared focus on ECM turnover during tissue development. Some immune/hormonal terms appear as ancillary signals, but the core theme is remodeling with morphogenetic processes.","confidence":"Medium","size":8,"edges":12,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0034769","count":2},{"id":"GO:0035593","count":2},{"id":"GO:0001913","count":2},{"id":"GO:0030574","count":2},{"id":"GO:0060441","count":2}]},{"hash":"33829899712240236","title":"Unknown","description":"The top GO terms span vascular regulation (negative regulation of vasculogenesis, VEGF signaling, endothelial differentiation) and a variety of metabolic and transport processes (phenylacetate/xanthine catabolism, nitrogen fixation, sodium transport, ferredoxin metabolism, ATP-linked electron transport, lactation), indicating no single cohesive function tying the proteins together. Confidence in a meaningful, specific label is None.","confidence":"","size":8,"edges":27,"triangles":50,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:2001213","count":5},{"id":"GO:0010124","count":5},{"id":"GO:0009115","count":5},{"id":"GO:0009399","count":5},{"id":"GO:0006814","count":5}]},{"hash":"341771994879007913","title":"Ubiquitin-Driven Protein Degradation and ERAD","description":"This cluster is enriched for ubiquitin-dependent protein catabolic processes, including autoubiquitination and K48-linked ubiquitination, as well as ER-associated degradation (ERAD). The co-occurrence of growth/regulatory terms like regulation of cell cycle and Wnt receptor catabolic process suggests a common theme of signaling protein turnover via ubiquitin-mediated degradation. This points to a cohesive role in tagging and directing proteins for degradation through ubiquitin-proteasome and ERAD pathways.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":6},{"id":"GO:0042787","count":6},{"id":"GO:0030433","count":6},{"id":"GO:0046621","count":5},{"id":"GO:0038018","count":5}]},{"hash":"728669932319788723","title":"Translation Machinery and Ribosome Biogenesis","description":"This cluster is strongly enriched for translation-related functions: cytoplasmic translation, general translation, tRNA modification and aminoacylation (glutaminyl/glutamyl), and ribosome biogenesis, including nuclear export of the large subunit and regulation of translational termination. Together these terms point to proteins involved in assembling and operating the ribosome and ensuring accurate protein synthesis, with a secondary note that some components may respond to antibiotics that target the translational machinery. ","confidence":"High","size":8,"edges":10,"triangles":3,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006400","count":2},{"id":"GO:0006412","count":2},{"id":"GO:0002181","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0006425","count":1}]},{"hash":"1588781749701324","title":"Innate immune signaling and chemokine production","description":"This cluster is dominated by terms related to innate immune signaling, notably NOD2 signaling and NF-kappaB regulation, as well as chemokine production (MIP-1 alpha, CCL5). Together these point to inflammatory signaling and chemokine-mediated responses, with other terms (e.g., cell migration or pain sensing) being related but less central. Overall, the set appears to reflect innate immune activation rather than a single, cohesive non-immune process. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032088","count":4},{"id":"GO:0070431","count":4},{"id":"GO:0086070","count":3},{"id":"GO:1903444","count":3},{"id":"GO:0016477","count":3}]},{"hash":"1854741917558883378","title":"Ubiquitin-dependent protein degradation","description":"This cluster is strongly enriched for GO terms related to ubiquitination and protein degradation (autoubiquitination, ubiquitin-dependent catabolic process, K48-linked ubiquitination, ERAD pathway) and includes related processes such as degradation of receptors and cell cycle regulation, suggesting a coherent theme of ubiquitin-mediated protein turnover. A few terms about X inactivation and peroxisome import are less central to this theme, but do not outweigh the dominant signal for ubiquitin-dependent degradation.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0070936","count":5},{"id":"GO:0038018","count":4},{"id":"GO:0046621","count":4}]},{"hash":"65946161633707370","title":"Plant Development and Hormone Signaling","description":"This cluster is dominated by GO terms tied to plant development (multicellular organism development, seed development, floral meristem growth) and hormone signaling (ethylene, abscisic acid pathways; auxin-related signaling). While a couple terms relate to general transcription regulation or metabolism (ubiquinone biosynthesis, insulin response), the overall pattern points to developmental processes in plants governed by hormone signaling. The proteins are not connected by edges here, but their annotations collectively reflect plant growth and regulatory pathways.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007275","count":2},{"id":"GO:0006744","count":2},{"id":"GO:0032869","count":2},{"id":"GO:0060774","count":1},{"id":"GO:0048316","count":1}]},{"hash":"738247056422982962","title":"DNA Repair and UV Protection","description":"This cluster\u2019s strongest GO terms are nucleotide-excision repair (GO:0006289) and UV protection (GO:0009650), pointing to a shared role in responding to DNA damage and UV-induced lesions. Other terms (Rho signaling, receptor recycling, hypoxia, embryonic development, and methylation-related terms) likely reflect annotation noise or multifunctional proteins, so the main theme is DNA repair/UV protection, though the signal is not uniformly strong across all items.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035023","count":2},{"id":"GO:0001881","count":2},{"id":"GO:0006306","count":1},{"id":"GO:0006289","count":1},{"id":"GO:0009650","count":1}]},{"hash":"328392266691786650","title":"P53-regulated cell cycle and protein stability","description":"Based on the enrichment of GO terms related to p53-mediated signaling, regulation of the cell cycle, protein stabilization, and modulation of ubiquitin-dependent degradation, this cluster appears to center on controlling cell cycle progression under stress and maintaining stability of key proteins, potentially via ubiquitin-proteasome regulation. The translation term is present but secondary to the core theme of cell cycle control and protein stability; the single cobalamin term is likely incidental. Overall, the cluster coherently maps to p53-associated cell cycle regulation and protein stabilization mechanisms.","confidence":"High","size":8,"edges":24,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:1901798","count":2},{"id":"GO:0071158","count":2},{"id":"GO:0071157","count":2},{"id":"GO:0050821","count":2}]},{"hash":"66778881695762253","title":"RNA Polymerase Transcription Initiation Complexes","description":"The terms cluster around DNA-templated transcription and multiple initiation events\u2014especially initiation at RNA Pol II promoters and preinitiation complex assembly, plus Pol III initiation\u2014indicating proteins that form or regulate the transcription initiation machinery for RNA polymerases II and III.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0001174","count":1},{"id":"GO:0090074","count":1}]},{"hash":"1333925313008080091","title":"ERAD Proteostasis and Aggresome Assembly","description":"The terms cluster around protein quality control in the endoplasmic reticulum, including ubiquitin-dependent ERAD, unfolded protein handling, chaperone-assisted refolding, and aggresome formation, all components of a proteostasis network. Some terms appear tangential or obsolete, but the core signal is clear: a module focused on maintaining protein homeostasis through folding, degradation, and sequestration of misfolded proteins.","confidence":"High","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1903071","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0070842","count":2},{"id":"GO:0070389","count":2},{"id":"GO:0051301","count":2}]},{"hash":"2058417442489660856","title":"Tissue differentiation and growth signaling","description":"This cluster centers on processes guiding cell fate and tissue remodeling, with terms for keratinocyte and fat cell differentiation, cell migration, and major growth-regulating pathways such as Wnt signaling and Hippo signaling. While apoptotic processes and responses to mechanical cues (muscle stretch) add some breadth, the common theme ties to differentiation and growth signaling in tissues. Confidence: Medium","confidence":"","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006915","count":4},{"id":"GO:0016477","count":3},{"id":"GO:0060044","count":3},{"id":"GO:0030216","count":3},{"id":"GO:0090263","count":3}]},{"hash":"733706992931448633","title":"Ubiquitin-regulated NF-\u03baB and JNK signaling","description":"The cluster\u2019s top GO terms point to NF-\u03baB pathway activation (I\u03baB phosphorylation, NF-\u03baB\u2013inducing kinase activity, TNF signaling) and ubiquitin-related regulation (ubiquitin-dependent ERAD, autoubiquitination). JNK cascade regulation and apoptosis modulation further support a theme of stress/inflammatory signaling modulated by ubiquitination. A few terms (e.g., dosage compensation, some obsolete terms) are less central, but the dominant signal is ubiquitin-mediated control of NF-\u03baB/JNK pathways.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":4},{"id":"GO:1903721","count":3},{"id":"GO:0042981","count":3},{"id":"GO:0070512","count":3},{"id":"GO:0046328","count":3}]},{"hash":"1968794663557543609","title":"Peroxisomal fatty acid metabolism","description":"The top terms are dominated by peroxisome-related processes (peroxisome-chloroplast tethering, protein import into peroxisome, and very long-chain fatty acid metabolism), suggesting a cohesive role in peroxisomal lipid metabolism, despite some unrelated terms in the list.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048147","count":1},{"id":"GO:0010381","count":1},{"id":"GO:0000038","count":1},{"id":"GO:0009640","count":1},{"id":"GO:0048137","count":1}]},{"hash":"1052738343806978195","title":"DNA replication and transcription machinery","description":"The strongest terms are DNA replication, DNA-templated transcription, and transcription regulation, indicating a genome maintenance/gene-expression theme; other terms indicate protein oligomerization and assembly and some organelle-related processes, which are likely secondary. This justifies a label focusing on DNA replication and transcription machinery.","confidence":"Medium","size":8,"edges":5,"triangles":0,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":5},{"id":"GO:0006351","count":4},{"id":"GO:0007118","count":3},{"id":"GO:0051260","count":2},{"id":"GO:0016562","count":2}]},{"hash":"1174557311249301066","title":"Embryogenesis with Metabolic and Epigenetic Regulation","description":"This cluster combines developmental processes (in utero embryonic development; primitive erythrocyte and megakaryocyte differentiation) with metabolism (thiamine and tetrahydrofolate pathways; mitochondrial electron transport) and chromatin/epigenetic regulation (DNA methylation, histone methylation, chromatin binding), suggesting a coordinated role of energy metabolism and epigenetic control during embryogenesis.","confidence":"Medium","size":8,"edges":13,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0009228","count":3},{"id":"GO:0046653","count":3},{"id":"GO:0010725","count":3},{"id":"GO:0043046","count":3}]},{"hash":"1325122347759433993","title":"Ribosome Biogenesis and Proteostasis","description":"The strongest signals are ribosome biogenesis and assembly of protein-containing complexes, pointing to production and assembly of ribosomal components. Coupled with SCF-dependent proteasomal ubiquitin-dependent protein catabolic process and deubiquitination, the cluster shows a coherent theme of ribosome-related biogenesis with regulated protein turnover. Other signals like signaling pathways (Wnt, NF-kappaB), zinc response, cobalamin biosynthesis, and viral process appear less prominently, suggesting they are secondary features rather than core functions of this cluster.","confidence":"Medium","size":8,"edges":3,"triangles":0,"max_degree":2,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0009236","count":3},{"id":"GO:0006461","count":3},{"id":"GO:0042254","count":2},{"id":"GO:0031146","count":1},{"id":"GO:0038061","count":1}]},{"hash":"314455729475652624","title":"Neural development with metabolic regulation","description":"This cluster includes explicit neural development terms (cerebellar cortex development, cerebral cortex development) along with related processes like cell migration and apoptotic processes. Metabolic terms (glucose metabolic process, positive regulation of triglyceride catabolic process) suggest accompanying metabolic regulation during development. Together, the predominant signal points to neural development with metabolic context.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045793","count":3},{"id":"GO:0021695","count":3},{"id":"GO:0048240","count":3},{"id":"GO:0006006","count":3},{"id":"GO:0021987","count":3}]},{"hash":"948134492046006065","title":"DNA replication and repair factors","description":"This cluster is driven by core genome maintenance functions: multiple terms point to DNA replication (GO:0006260), mitotic DNA replication checkpoint signaling (GO:0033314), and UV-damage excision repair (GO:0070914). Additionally, translesion synthesis (GO:0070987) and related repair pathways support genome stability. Protein oligomerization/assembly terms (GO:0051260, GO:0034214) fit with multi-subunit repair/replication complexes. Some terms about peroxisome import or mitochondrial complex III assembly are less central and may reflect broader protein assembly roles, but the dominant theme is DNA replication and repair. ","confidence":"Medium","size":8,"edges":7,"triangles":2,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0051260","count":2},{"id":"GO:0016562","count":2},{"id":"GO:0034214","count":2},{"id":"GO:0034551","count":2}]},{"hash":"1941676536423488159","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":3,"triangles":0,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0000462","count":4},{"id":"GO:0000463","count":4},{"id":"GO:0042273","count":4},{"id":"GO:0000398","count":4},{"id":"GO:0000480","count":4}]},{"hash":"551251370298294177","title":"Peroxisomal lipid and energy metabolism","description":"The GO terms cluster around lipid biosynthesis (phospholipids, glycerophospholipids, triglycerides), energy and redox processes (NADPH regeneration, glycerol-3-phosphate shuttle, gluconeogenesis, pantothenate/CoA biosynthesis), and a peroxisomal matrix import role, pointing to peroxisome-associated lipid metabolism and energy balance. A few defense-related terms may reflect broader plant physiology but are less central to the main theme.","confidence":"Medium","size":8,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090038","count":2},{"id":"GO:0009627","count":2},{"id":"GO:0008654","count":2},{"id":"GO:0019432","count":2},{"id":"GO:0006650","count":2}]},{"hash":"263877569718351670","title":"Chromatin-Mediated Transcription Regulation","description":"The top GO terms cluster around transcription control by RNA polymerase II and chromatin modifications, including histone ubiquitination/acetylation and nucleosome positioning, indicating regulation of transcription via epigenetic chromatin state.","confidence":"High","size":8,"edges":7,"triangles":2,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":2},{"id":"GO:0000122","count":2},{"id":"GO:0001178","count":2},{"id":"GO:0071441","count":2},{"id":"GO:0042766","count":2}]},{"hash":"1495525483803674199","title":"Cilium assembly and ubiquitin-regulated mitosis","description":"This cluster centers on cilium formation (GO:0060271) and mitotic regulation, with multiple ubiquitin-related processes (polyubiquitination, ubiquitin-dependent proteolysis) supporting cell cycle control. The visual perception term likely reflects ciliary function in photoreceptors, linking sensory biology to ciliary and mitotic regulation through ubiquitination and protein turnover.","confidence":"Medium","size":8,"edges":7,"triangles":4,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0007601","count":7},{"id":"GO:0000278","count":7},{"id":"GO:0008285","count":5},{"id":"GO:0031571","count":5},{"id":"GO:0071276","count":5}]},{"hash":"990545265540571951","title":"Ubiquitin-mediated protein degradation","description":"GO terms predominantly point to ubiquitination and degradation pathways, including polyubiquitination, ubiquitin-dependent protein catabolic process, and ERAD-related pathways, as well as degradation of receptors (Wnt). Additional terms touching cell cycle and signaling regulation fit with proteostasis-driven control of growth and signaling. Overall, the cluster appears to group proteins involved in ubiquitin-dependent turnover and turnover-regulated signaling. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051096","count":2},{"id":"GO:0071157","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0042787","count":1},{"id":"GO:0046621","count":1}]},{"hash":"930987863897248137","title":"Transmembrane Transporters for Ions and Nutrients","description":"The top GO terms are dominated by various transmembrane transport activities for a range of substrates (nitrate, nitrite, arabinose, sodium, phosphate, fucose, vitamins) and related assimilation processes, plus a term for neurotransmitter loading into synaptic vesicles. This points to a cluster of membrane transporter proteins mediating uptake and handling of diverse solutes across membranes, rather than a single substrate. The vesicular transport term reinforces involvement in membrane-associated handling of cargo. Hence, a concise label capturing this transporter-focused, multi-substrate theme is appropriate.","confidence":"High","size":8,"edges":11,"triangles":4,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0015707","count":2},{"id":"GO:0042891","count":2},{"id":"GO:0035725","count":2}]},{"hash":"72495900237743900","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000480","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0000472","count":1},{"id":"GO:0080022","count":1},{"id":"GO:0055121","count":1}]},{"hash":"492670448585972344","title":"Amino acid metabolism cluster","description":"Dominated by amino acid biosynthesis terms (tyrosine, proline, valine, isoleucine) plus cofactor and vitamin synthesis (pantothenate, NADPH regeneration), with some catabolic and transport terms. This indicates a general metabolic cluster with emphasis on amino acid production rather than a single specific pathway.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009097","count":2},{"id":"GO:0046392","count":2},{"id":"GO:0019310","count":2},{"id":"GO:0006571","count":2},{"id":"GO:0006740","count":2}]},{"hash":"585833698307606292","title":"Signaling-Responsive Splicing and Development","description":"The top GO terms point to cellular responses to signaling molecules (transforming growth factor beta, tumor necrosis factor, retinoic acid) and developmental processes (hematopoietic stem cell differentiation, larval salivary gland morphogenesis), together with regulation of mRNA splicing via the spliceosome and protein folding/chaperone-related processes. This suggests a theme where signaling cues influence gene expression through splicing regulation and developmental pathways, with some involvement in protein homeostasis. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071560","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0071356","count":1},{"id":"GO:0060218","count":1},{"id":"GO:1904715","count":1}]},{"hash":"1570226993419948842","title":"Unknown","description":"The top terms span extremely diverse processes (RNA splicing/transport, hypoxia response, cell cycle, various kinase/GTPase regulatory activities, GPCR signaling, and even bioluminescence) with no coherent shared function, and there are no edges linking proteins, suggesting no single theme. Therefore, no reliable functional label can be assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008218","count":2},{"id":"GO:0000398","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0071902","count":2},{"id":"GO:0051028","count":2}]},{"hash":"50942522800618845","title":"Heat Stress and ER Protein Folding","description":"These proteins show a strong enrichment for heat-related responses and protein quality control in the endoplasmic reticulum, including response to heat, unfolded protein response, and ER protein folding, pointing to a shared role in maintaining protein homeostasis under heat stress. While a couple of terms (e.g., DNA replication, developmental signaling) are present, the predominant theme is heat-induced protein folding and ER chaperone activity, justifying this label.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1900035","count":2},{"id":"GO:1901621","count":2},{"id":"GO:0034975","count":2}]},{"hash":"1200335173613877573","title":"RNA Metabolism and Ribosome Biogenesis","description":"The cluster includes GO terms spanning transcription regulation (termination of RNA Pol II, start-site selection) and chromatin-related processes, along with ribosome biogenesis (cytosolic and mitochondrial large subunit assembly), plus cytoplasmic RNA handling (stress granule localization and post-transcriptional gene silencing). This combination suggests a group of proteins linked to RNA metabolism from transcription through to ribosome assembly and translation control, hence the label.","confidence":"Medium","size":8,"edges":28,"triangles":56,"max_degree":7,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0006369","count":5},{"id":"GO:0071441","count":3},{"id":"GO:0001178","count":3},{"id":"GO:1903608","count":3},{"id":"GO:0060303","count":3}]},{"hash":"1087064686090746118","title":"RNA processing and turnover","description":"The cluster shows enrichment for mRNA splicing (spliceosome), pre-miRNA processing, miRNA catabolic process, and mRNA decay/turnover, plus RNA stabilization and transcription termination regulation. This points to a group of proteins involved in post-transcriptional RNA processing and RNA stability rather than a single signaling pathway. A few terms (osmotic stress\u2013related apoptosis, kidney development) appear less central and may be incidental. ","confidence":"Medium","size":8,"edges":24,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":2},{"id":"GO:1902219","count":1},{"id":"GO:0090503","count":1},{"id":"GO:0010587","count":1},{"id":"GO:0031054","count":1}]},{"hash":"560837989656844868","title":"Carbohydrate Catabolism","description":"The GO terms cluster around glycolysis and carbohydrate-derived carbon utilization (glycol catabolic process, L-fucose/glycerol catabolism, carbon utilization), suggesting a shared role in breaking down carbohydrates for energy; a few terms are obsolete or peripheral noise, but the core theme is carbohydrate metabolism.","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0060325","count":1},{"id":"GO:0097202","count":1},{"id":"GO:0042264","count":1},{"id":"GO:0071271","count":1},{"id":"GO:0015993","count":1}]},{"hash":"345174264454127989","title":"ER Proteostasis Under Heat Stress","description":"The cluster is enriched for GO terms tied to heat response, unfolded protein response, and ER protein folding, pointing to a shared role in managing protein quality control under thermal stress. Some terms like negative regulation of kinase activity and protein oligomerization may reflect regulatory and assembly aspects of proteostasis.","confidence":"Medium","size":8,"edges":18,"triangles":19,"max_degree":7,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":8},{"id":"GO:0009408","count":7},{"id":"GO:0006260","count":7},{"id":"GO:1900035","count":7},{"id":"GO:1901621","count":7}]},{"hash":"1942446762771251254","title":"Multitissue Development and Differentiation","description":"Although one term highlights DNA replication, the majority of the top GO terms describe development and differentiation across several tissues (thymus, inner ear, thyroid, mesoderm, Bergmann glia, keratinocytes). This suggests the cluster groups proteins involved in general developmental processes and tissue-specific differentiation rather than a single conserved pathway.","confidence":"Medium","size":8,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0048538","count":5},{"id":"GO:0048839","count":5},{"id":"GO:1901621","count":5},{"id":"GO:0060044","count":5}]},{"hash":"1137513830694998696","title":"Folate and thiamine transporter cluster","description":"This cluster is dominated by transmembrane transport terms for vitamins (folate/folic acid, methotrexate, thiamine), pointing to a vitamin transporter function as the core theme; the additional regulatory terms (cell cycle, TLR signaling, transcriptional regulation, apoptosis, necroptosis, polyubiquitination) likely reflect broader roles or annotation noise rather than a shared primary function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098838","count":1},{"id":"GO:0051958","count":1},{"id":"GO:0015884","count":1},{"id":"GO:0071934","count":1},{"id":"GO:0071157","count":1}]},{"hash":"2053742398529982646","title":"Neurovascular and cardiac development signaling","description":"The terms point to development and signaling across nervous and cardiovascular systems: axonogenesis, synaptic plasticity, heart development, and branching in vessel morphogenesis, with regulatory kinase and guanylate cyclase activities supporting signaling roles.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007409","count":3},{"id":"GO:0006469","count":3},{"id":"GO:2001246","count":2},{"id":"GO:0009268","count":2},{"id":"GO:0001569","count":2}]},{"hash":"99300567500206266","title":"Neural development and brain region differentiation","description":"This cluster is enriched for brain-related developmental terms, notably cerebral cortex development and substantia nigra development, along with positive regulation of stem cell proliferation, which points to neural lineage specification and brain region differentiation. While some metabolic terms are present (glutathione metabolism, thymidine and thiamine processes), the dominant signal centers on neural development and differentiation rather than a single metabolic pathway, supporting a brain-development-focused label.","confidence":"Medium","size":8,"edges":4,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0021987","count":3},{"id":"GO:2000648","count":3},{"id":"GO:0006605","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0046886","count":2}]},{"hash":"1268380324738922180","title":"Mitotic spindle assembly and microtubule dynamics","description":"The cluster is dominated by GO terms related to microtubule organization and mitosis (cytoplasmic microtubule organization, spindle pole body duplication, spindle midzone assembly, microtubule nucleation, cell division, cytokinesis), suggesting proteins involved in mitotic spindle function and microtubule dynamics. A few terms (interleukin-4 response, neuron migration) are peripheral or context-dependent, but do not outweigh the core mitotic/microtubule theme.","confidence":"High","size":8,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0031122","count":4},{"id":"GO:1903087","count":4},{"id":"GO:0071353","count":4},{"id":"GO:0051256","count":4},{"id":"GO:2000767","count":4}]},{"hash":"762159214463156641","title":"Amino acid biosynthesis and related metabolism","description":"This cluster is dominated by amino acid biosynthesis terms (serine, threonine, isoleucine) and related small-molecule pathways (2-oxobutyrate, cyanide metabolism, coenzyme M biosynthesis), implying a core function in amino acid metabolism and associated cofactors. Some annotations like response to morphine may reflect annotation noise.","confidence":"Medium","size":8,"edges":26,"triangles":45,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0043278","count":4},{"id":"GO:0042866","count":4},{"id":"GO:0009097","count":4},{"id":"GO:0019499","count":4},{"id":"GO:0018871","count":4}]},{"hash":"1325141617055241999","title":"Neurodevelopmental Signaling and Trafficking","description":"This cluster centers on neural development and signaling, with terms like formation of radial glial scaffolds and interneuron migration, plus related signaling pathways (acetylcholine GPCR, EGFR). It also includes membrane trafficking (Golgi to plasma membrane transport) and lysosomal organization, suggesting joint roles in developing neurons. Some terms (heart development, melanocyte differentiation) appear more peripheral but don\u2019t dominate the set. ","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021943","count":3},{"id":"GO:0043001","count":3},{"id":"GO:0007507","count":3},{"id":"GO:0045634","count":3},{"id":"GO:0042711","count":3}]},{"hash":"2068479940973316172","title":"RNA and Histone Methylation Regulators","description":"This cluster is enriched in methylation-related GO terms: rRNA methylation (GO:0031167), rRNA guanine-N7 methylation (GO:0070476), 7-methylguanosine mRNA capping (GO:0006370), histone H4-R3 methylation (GO:0043985), and arginine methylation (GO:0019919). It also includes transcription regulation by RNA Pol II (GO:0000122) and growth/senescence terms (GO:0016049, GO:0090398), suggesting a set of proteins involved in RNA processing and chromatin modification that influence gene expression and cell fate. The presence of cobalamin biosynthesis and xenobiotic response hints at broader regulatory roles, but the core signal centers on methylation-based control of RNA and chromatin.","confidence":"Medium","size":8,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031167","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0043985","count":2},{"id":"GO:0016049","count":2},{"id":"GO:0090398","count":2}]},{"hash":"1411441928196041674","title":"DNA replication and genome maintenance","description":"Most terms cluster around DNA replication, cell cycle checkpoints during replication, and DNA repair (UV-damage excision repair, translesion synthesis, mitotic replication checkpoint). A few terms describe protein oligomerization and organelle assembly, which are more structural and less defining for the cluster\u2019s core function. Overall, the dominant theme is genome maintenance during replication/repair.","confidence":"High","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:0051260","count":1},{"id":"GO:0016562","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0034214","count":1}]},{"hash":"1443703441005187102","title":"Membrane Transport of Diverse Substrates","description":"Top GO terms cluster around membrane transport of various substrates (heme, xenobiotics, teichoic acids, ions, fatty acids), suggesting a transport-focused group; a few outliers (nucleotide-excision repair, ABA signaling) are present but do not redefine the cluster.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015886","count":2},{"id":"GO:0046618","count":1},{"id":"GO:0060081","count":1},{"id":"GO:1901527","count":1},{"id":"GO:0006289","count":1}]},{"hash":"1039274733711868702","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":9,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0009718","count":3},{"id":"GO:0030435","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0033358","count":2}]},{"hash":"636291260050137960","title":"Metabolic Regulation of Development","description":"This cluster features metabolism-related GO terms (thiamine biosynthetic process, dihydrolipoamide metabolic process) alongside development-related terms (neuron maturation, positive regulation of stem cell proliferation, erythrocyte differentiation), suggesting proteins that link metabolic activity to cellular differentiation and growth. While there are some stress-related terms, the combination points to a theme of metabolism supporting developmental processes.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0009409","count":3},{"id":"GO:0046886","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0045648","count":2}]},{"hash":"1440105219052860831","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0042619","count":3},{"id":"GO:0097089","count":2},{"id":"GO:1902181","count":2},{"id":"GO:0042400","count":2}]},{"hash":"533983479072819252","title":"Golgi UDP-sugar transporters and Mg2+ transport","description":"This cluster centers on transmembrane transport: ions (Mg2+) and sugar nucleotides (UDP-galactose, UDP-GlcNAc) into membranes/organelles like the Golgi, plus a broader sugar transport term (sialic acid). The strongest signals are Golgi nucleotide-sugar import terms, suggesting a group of transporter proteins involved in glycosylation-related trafficking, with Mg2+ transport as a related membrane transport activity. Confidence: Medium","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903830","count":1},{"id":"GO:0010961","count":1},{"id":"GO:0071286","count":1},{"id":"GO:0097624","count":1},{"id":"GO:1990569","count":1}]},{"hash":"1859811291929584693","title":"Biosynthesis of vitamins and secondary metabolites","description":"The top GO terms cluster around biosynthetic processes for vitamins (biotin, menaquinone, vitamin E), polyamines, and secondary metabolites like alkaloids and antibiotics, suggesting the proteins participate in diverse metabolite biosynthesis. Some terms related to RNA processing and xenobiotic response are present but appear peripheral to the main theme, indicating the primary signal is metabolite biosynthesis. This label captures the common function without overfitting to a single pathway.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0009234","count":2},{"id":"GO:0009820","count":2},{"id":"GO:0006370","count":2}]},{"hash":"249002194152251836","title":"Differentiation and Growth Regulation","description":"The cluster\u2019s top GO terms include brown fat cell differentiation, pollen sperm cell differentiation, and negative regulation of multicellular organism growth. While these terms span different cell types and species, they collectively point to broad developmental processes\u2014growth control and cellular differentiation\u2014rather than a single, cohesive pathway. The sparse term counts and lack of interactions support a general developmental category rather than a specific function.","confidence":"Low","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0040015","count":1},{"id":"GO:0050873","count":1},{"id":"GO:0048235","count":1}]},{"hash":"462318901941313776","title":"Unknown","description":"The top GO terms span diverse and unrelated processes\u2014from microbial metabolite biosynthesis to vertebrate hormone metabolism and development\u2014offering no single coherent function to bind the cluster, so a specific label is not justifiable.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042619","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0042264","count":2},{"id":"GO:0008209","count":1}]},{"hash":"2128686366549854569","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0033358","count":1},{"id":"GO:0009718","count":1},{"id":"GO:0042351","count":1},{"id":"GO:0080110","count":1}]},{"hash":"473434637124126202","title":"Unknown","description":"Top GO terms are a mixed bag: hormone metabolism (androgen and glucocorticoid processes) coexists with various catabolic and developmental processes, plus a regulatory transcription term and some obsolete annotations. The lack of a unifying biological theme, along with zero edges among members, suggests this cluster may reflect annotation noise or heterogeneous functions rather than a coherent pathway. Therefore a specific, confident label cannot be assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0042208","count":2},{"id":"GO:0034720","count":2},{"id":"GO:0008209","count":1},{"id":"GO:0006355","count":1}]},{"hash":"1329253863939108105","title":"Mitochondrial lipid biosynthesis and remodeling","description":"The proteins show a coherent focus on lipid metabolism and mitochondrial membrane processes, with GO terms for mitochondrial ATP synthesis, CDP-diacylglycerol biosynthesis, cardiolipin acyl-chain remodeling, ether lipid and glycerophospholipid biosynthesis, and related lipid signaling (e.g., platelet activating factor biosynthesis). Although a few terms are more peripheral (e.g., cerebellum morphogenesis, cutin biosynthesis), the dominant pattern points to lipid production and remodeling in a mitochondrial context. ","confidence":"High","size":8,"edges":24,"triangles":36,"max_degree":7,"top_function":null,"top_go_terms":[{"id":"GO:0021587","count":2},{"id":"GO:0042775","count":2},{"id":"GO:0019432","count":2},{"id":"GO:0002071","count":2},{"id":"GO:0010143","count":2}]},{"hash":"1949813969387354886","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0080110","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0019305","count":2}]},{"hash":"1080411271811876603","title":"Ribosome Biogenesis and Translation","description":"Top terms are dominated by ribosome biogenesis and translation (including ribosomal small subunit biogenesis), indicating proteins involved in ribosome assembly and protein synthesis. Some additional terms (cell cycle, MAPK signaling, nephric duct morphogenesis) appear but are less represented, so the core function is ribosome-related. ","confidence":"Medium","size":8,"edges":2,"triangles":0,"max_degree":2,"top_function":"ribosome biogenesis","top_go_terms":[{"id":"GO:0042254","count":3},{"id":"GO:0006412","count":3},{"id":"GO:0042274","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0051301","count":2}]},{"hash":"551626849063701009","title":"Unknown","description":"The Top Terms are highly diverse (ubiquitination, nuclear export, immune signaling, various developmental processes, and even plant-specific phototropism), with no clear shared function or pathway linking the proteins. Edges are also absent, so there isn\u2019t a cohesive theme to name a specific function cluster.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046825","count":2},{"id":"GO:1990390","count":1},{"id":"GO:0050853","count":1},{"id":"GO:0031397","count":1},{"id":"GO:0007519","count":1}]},{"hash":"1924172600092192551","title":"Transmembrane solute transporters","description":"The cluster\u2019s GO terms are centered on transmembrane transport of various solutes (ions, nitrite/nitrate, sugars like fucose and galactose, vitamins, xenobiotics) and vesicular neurotransmitter loading, indicating a cohesive set of membrane transporter proteins handling diverse molecules across membranes and into synaptic vesicles.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035435","count":5},{"id":"GO:0006855","count":5},{"id":"GO:0015707","count":4},{"id":"GO:0015706","count":4},{"id":"GO:0006004","count":4}]},{"hash":"106588434781821536","title":"Proteostasis and Heat Shock Response","description":"Most terms center on protein folding, ER folding, unfolded protein response, and proteasome-mediated quality control, suggesting a proteostasis-focused cluster influenced by heat stress; a few terms touch on related processes like oligomerization, but the dominant theme is protein homeostasis under stress.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":1},{"id":"GO:0006260","count":1},{"id":"GO:1900035","count":1},{"id":"GO:1901621","count":1},{"id":"GO:0034975","count":1}]},{"hash":"2177402677352784645","title":"Vacuolar ion transport and homeostasis","description":"The top GO terms point to vacuole-related processes (vacuolar acidification, vacuole organization, protein targeting to vacuole) and ion transport (sodium and proton) with energy coupling (proton motive force-driven ATP synthesis) and copper ion homeostasis, suggesting a core theme of vacuolar function tied to ion transport and homeostasis. Some terms like photosystem II assembly and leucine biosynthesis are less directly related, likely annotation noise or broader metabolic links, but do not override the main vacuolar/ion transport signal.","confidence":"Medium","size":8,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006626","count":1},{"id":"GO:0007035","count":1},{"id":"GO:0007033","count":1},{"id":"GO:0006623","count":1},{"id":"GO:0006814","count":1}]},{"hash":"569866719286977139","title":"Unknown","description":"The top GO terms span multiple disparate themes: several entries relate to detection of sensory stimuli (mechanical, chemical, temperature) and inflammatory/chemokine signaling, while others touch on endothelial remodeling and unrelated stress responses (e.g., mercury ion response, brown fat regulation). There isn't a clear, single biological process tying these functions together, so a concise, cohesive label is not supported.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046689","count":2},{"id":"GO:1903444","count":2},{"id":"GO:0071642","count":2},{"id":"GO:0050966","count":2},{"id":"GO:0071651","count":2}]},{"hash":"1957247240054225974","title":"Unknown","description":"The terms cover diverse processes (hormone response, kidney development and function, endocytosis, lipid catabolism, and signaling regulation) with no single unifying function, so a specific label cannot be assigned.","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031953","count":1},{"id":"GO:0071392","count":1},{"id":"GO:0006898","count":1},{"id":"GO:0045765","count":1},{"id":"GO:0006685","count":1}]},{"hash":"1810389505046144245","title":"RNA and protein methylation enzymes","description":"Top GO terms show multiple methylation processes (rRNA, arginine, glutamine, histone), indicating a cluster centered on methyltransferase activities affecting RNA and proteins; other biosynthetic terms are present but secondary. Confidence: High","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":4},{"id":"GO:0016049","count":4},{"id":"GO:0019919","count":4},{"id":"GO:0043985","count":4},{"id":"GO:0046690","count":4}]},{"hash":"2122497947443505661","title":"Seed lipid metabolism","description":"GO terms cluster around fatty acid biosynthesis and metabolism, including long/very long-chain fatty acids and transport, with seed-related development terms (seed coat development, germination) linking lipid metabolism to seed biology; together they suggest a lipid-centered cluster with seed associations, though a few broader catabolic terms are present.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010124","count":1},{"id":"GO:0001579","count":1},{"id":"GO:0043041","count":1},{"id":"GO:0006633","count":1},{"id":"GO:0090410","count":1}]},{"hash":"421241538927499585","title":"Diverse Metabolite Biosynthesis","description":"This cluster is enriched for multiple biosynthetic processes\u2014biotin, antibiotic, menaquinone, polyamine, and vitamin E biosynthesis\u2014suggesting a grouping around the production of diverse metabolites. While there are some peripheral terms (aerobic respiration, xenobiotic response, mRNA capping), the dominant theme centers on biosynthesis across metabolite classes, justifying the label.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0009234","count":3},{"id":"GO:2000124","count":3},{"id":"GO:0019433","count":3}]},{"hash":"98479907905768219","title":"Plant Development and Hormone Signaling","description":"The GO terms cluster around plant growth and development (seed development, floral meristem growth, multicellular organism development) and hormone signaling (ABA-activated and ethylene-activated pathways), with transcription regulation also represented. This suggests a cohesive theme of developmental processes regulated by plant hormones, despite a single defense-related term present. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060774","count":1},{"id":"GO:0048316","count":1},{"id":"GO:1901959","count":1},{"id":"GO:0009738","count":1},{"id":"GO:0009873","count":1}]},{"hash":"114001481307839700","title":"Chromatin remodeling and transcription regulation","description":"The cluster\u2019s top GO terms are dominated by chromatin remodeling, regulation of transcription start site selection, and histone acetylation regulation. While a few terms touch on ribosome assembly and post-transcriptional silencing, the central theme appears to be chromatin structure modification and transcriptional control.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":3},{"id":"GO:0071441","count":2},{"id":"GO:0001178","count":2},{"id":"GO:0060303","count":2},{"id":"GO:1902775","count":2}]},{"hash":"1245216117561860036","title":"Developmental differentiation and growth signaling","description":"This cluster shows enrichment for differentiation-related GO terms (lung epithelial and neuron differentiation) and regulation of TGF-beta signaling, pointing to roles in developmental processes and growth-control signaling. While some terms touch on vascular morphogenesis and metabolic/stress responses, the strongest signals center on differentiation and signaling regulation, suggesting a broad developmental/regulatory theme rather than a single focused function.","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060487","count":2},{"id":"GO:0030182","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0030512","count":2},{"id":"GO:0001569","count":1}]},{"hash":"160075664061979599","title":"Diverse membrane substrate transport","description":"GO terms cluster around transport/export of diverse substrates across membranes (xenobiotics, lipids, peptides, acids, drugs), with several subtypes (peroxisomal fatty acid import, ceramide translocation, taurine transport, daunorubicin transport, teichoic acid transport, bacteriocin transport, oligopeptide export). The overall theme is membrane-associated transport, though nucleotide-excision repair appears as an outlier. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046618","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0015910","count":2},{"id":"GO:0015777","count":2},{"id":"GO:0043213","count":2}]},{"hash":"1036380556901176885","title":"Cell signaling and membrane trafficking","description":"The top GO terms cluster around signaling and membrane-associated processes (Wnt signaling; regulation of endocytosis; protein localization at the plasma membrane) with additional notes on cell migration and related signaling. While there are some immune and sensory terms present, the common thread appears to be signaling events that are coordinated with membrane trafficking and localization. Hence, a concise label is \u201cCell signaling and membrane trafficking.\u201d","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016055","count":2},{"id":"GO:0048549","count":2},{"id":"GO:0086070","count":1},{"id":"GO:1903444","count":1},{"id":"GO:0016477","count":1}]},{"hash":"2084538700641281634","title":"Acetylation-Related Protein Modifications","description":"The cluster is strongly enriched for acetylation-related GO terms, including N-terminal acetylation, peptidyl-lysine acetylation, spermine acetylation, and propionylation, pointing to a core theme of acetyltransferase activity and acetylation-based regulation. Other terms like sporulation and leaf formation appear peripheral, likely reflecting broader regulatory contexts rather than a single cohesive function.","confidence":"Medium","size":8,"edges":12,"triangles":5,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0030435","count":5},{"id":"GO:0009447","count":5},{"id":"GO:0018003","count":5},{"id":"GO:2000025","count":5},{"id":"GO:0006044","count":5}]},{"hash":"583235663476987152","title":"Unknown","description":"Unknown","confidence":"","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031126","count":2},{"id":"GO:0090503","count":2},{"id":"GO:0034414","count":2},{"id":"GO:0006364","count":2},{"id":"GO:0019243","count":2}]},{"hash":"272458166475848473","title":"mRNA Decay and P-Body Assembly","description":"Dominant GO terms point to cytoplasmic mRNA turnover: deadenylation-dependent decay, poly(A) tail shortening, exonucleolytic hydrolysis, and decapping, along with P-body assembly and miRNA-mediated post-transcriptional silencing; together these reflect post-transcriptional regulation of mRNA and its storage/decay sites. An outlier GO term for cell wall organization likely reflects noise rather than core function. ","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":2},{"id":"GO:0000288","count":1},{"id":"GO:0000289","count":1},{"id":"GO:0090503","count":1},{"id":"GO:0033962","count":1}]},{"hash":"119950118780520671","title":"Chlorophyll and quinone/vitamin K biosynthesis","description":"The cluster is dominated by GO terms for chlorophyll biosynthesis and multiple quinone/vitamin K biosynthetic processes (phylloquinone, plastoquinone, menaquinone, vitamin K), suggesting a cohesive theme of photosynthetic pigment and cofactor production. Some metal/oxidative stress and transcription regulation terms are present but less central to the core function.","confidence":"High","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046521","count":1},{"id":"GO:0046689","count":1},{"id":"GO:0071248","count":1},{"id":"GO:0045893","count":1},{"id":"GO:0006979","count":1}]},{"hash":"1308135553989951595","title":"Cardiohepatic development and metabolism","description":"The top GO terms center on organ development, notably heart and liver development, with additional developmental context like post-embryonic development. Intersecting these are metabolic processes such as threonine and glutamine metabolism and fatty acid beta-oxidation, plus general phosphorylation, suggesting proteins involved in cardiohepatic development together with metabolic activity. While some terms are obsolete, the dominant signal points to development of heart and liver accompanied by metabolism. ","confidence":"Medium","size":8,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0007507","count":2},{"id":"GO:0009088","count":2},{"id":"GO:0006541","count":2},{"id":"GO:0033540","count":1}]},{"hash":"328987316412952456","title":"Ubiquitin-Dependent Protein Regulation","description":"This cluster centers on ubiquitination processes\u2014deubiquitination, autoubiquitination, and ubiquitin-dependent ERAD\u2014pointing to a shared theme of ubiquitin-mediated protein regulation. While some terms touch on transcription regulation, chromatin modification, and nuclear transport, these often arise downstream of ubiquitin signaling and proteostasis, suggesting a cohesive focus on ubiquitin-dependent control of protein fate and gene expression.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016579","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0010286","count":2},{"id":"GO:0043392","count":2}]},{"hash":"2222909851951685213","title":"Ribosome Biogenesis and RNA Processing","description":"Top GO terms cluster around ribosome production and RNA maturation, including ribosome biogenesis, ribosomal large subunit export from nucleus, and tRNA modification, suggesting a shared function in assembling and processing the cellular translation machinery. Additional terms point to related cell cycle/division processes, and despite a stray term like pituitary gland development, the dominant theme is ribosome assembly and RNA processing rather than signaling or developmental specificity.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021983","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0006915","count":2},{"id":"GO:0042254","count":1},{"id":"GO:0006400","count":1}]},{"hash":"2034333706402509786","title":"Steroid Hormone Biosynthesis and Oxidative Stress Response","description":"The top GO terms point to steroid-related metabolism (bile acid biosynthesis, C21-steroid hormone biosynthetic process, androgen metabolic process) alongside oxidative stress signaling (response to hydrogen peroxide, prostaglandin D stimulus, stress-activated MAPK cascade). While a couple terms are less related (naphthalene catabolic process, tissue homeostasis), the dominant pattern is steroid/lipid metabolism coupled with stress response, justifying this label.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":4},{"id":"GO:0070301","count":2},{"id":"GO:0071799","count":1},{"id":"GO:0001894","count":1},{"id":"GO:0006699","count":1}]},{"hash":"363247617206852312","title":"Ubiquitin-Dependent Proteolysis and Growth Signaling","description":"This cluster is dominated by ubiquitin-related catabolic processes (ubiquitin-dependent protein catabolic, protein autoubiquitination, histone catabolic), alongside terms tied to NF-kappaB and Wnt signaling and growth regulation. The common thread is proteins involved in tagging substrates for degradation and modulating signaling pathways that control cell growth, apoptosis, and chromatin dynamics. A few items may reflect broader chromatin regulation, but the core signal points to ubiquitin-mediated turnover and its impact on growth-related signaling.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042787","count":4},{"id":"GO:0036205","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0090073","count":3},{"id":"GO:1903721","count":3}]},{"hash":"994647621943464024","title":"Ubiquitin-mediated protein turnover","description":"The top GO terms are dominated by ubiquitination-related processes (autoubiquitination, K48- and K6-linked ubiquitination, and monoubiquitination) and ubiquitin-dependent protein catabolic processes, plus histone catabolism. This points to a cluster centered on the ubiquitin-proteasome system that tags and degrades proteins, including regulatory histones, and modulates signaling pathways such as TNF and CD40 signaling. The co-occurrence of these ubiquitination and degradation terms suggests a cohesive function in protein turnover and its impact on immune signaling.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:1903265","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0070936","count":4},{"id":"GO:0036205","count":4},{"id":"GO:0042787","count":4}]},{"hash":"906631806289837420","title":"Oxidative Detoxification and Stress Response","description":"This cluster is enriched for detoxification and redox-related processes (cellular oxidant detoxification, glutathione metabolism, detoxification of nitrogen compounds) and stress-related signaling (insulin response, prostaglandin biosynthesis). While there are additional terms like nucleotide-excision repair and translation elongation, the common thread appears to be cellular defense against oxidative/chemical stress and related metabolic responses, making this label representative. ","confidence":"Medium","size":7,"edges":21,"triangles":35,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":6},{"id":"GO:0006749","count":5},{"id":"GO:0043200","count":5},{"id":"GO:0042994","count":5},{"id":"GO:0014003","count":5}]},{"hash":"309601367794160802","title":"Ubiquitin-Dependent Protein Degradation","description":"The top GO terms are dominated by ubiquitination-related processes (autoubiquitination; K63-, K48-, K6-linked ubiquitination) and ubiquitin-dependent proteolysis/ERAD, indicating a cluster centered on tagging proteins for degradation or regulation via ubiquitin. Additional terms related to proteostasis regulation (chaperone-mediated complex assembly) and signaling (TNF-mediated pathways) support a broader ubiquitin-driven quality control and signaling role. Despite the presence of a histone catabolic term, the overarching theme is ubiquitin tagging leading to degradation or proteostasis control.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0070534","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0036205","count":2},{"id":"GO:0033132","count":2}]},{"hash":"2007370991685820729","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":18,"triangles":23,"max_degree":6,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:1903608","count":4},{"id":"GO:1902775","count":4},{"id":"GO:1904570","count":4},{"id":"GO:0042255","count":4},{"id":"GO:0016441","count":4}]},{"hash":"861117788189749291","title":"Muscle development and stretch response","description":"This cluster's top GO terms concentrate on skeletal muscle development, response to muscle stretch, and related tissue remodeling (cell migration). While there are other general terms (mRNA processing, telomere regulation) present at lower emphasis, the prominent muscle-associated processes suggest a muscle development/stretch-response theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0035994","count":3},{"id":"GO:0045444","count":3},{"id":"GO:0032212","count":3},{"id":"GO:0006397","count":3}]},{"hash":"770109052934848981","title":"Plant transcriptional regulation and developmental signaling","description":"The top GO terms include DNA-templated transcription and nuclear export regulation, plus plant-specific processes like meristem identity maintenance and photosystem stoichiometry adjustment, suggesting a cluster centered on transcriptional control during plant development and light-related regulation. Additional signals about TGF-beta and NF-kappaB pathway modulation and phosphatase activity indicate coordinated regulation of signaling and transcription. ","confidence":"Medium","size":7,"edges":8,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0030512","count":1},{"id":"GO:0035970","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0046827","count":1}]},{"hash":"853351844935454645","title":"Cell wall polysaccharide biosynthesis","description":"This cluster centers on biosynthetic processes for polysaccharides and cell wall components (slime layer and extracellular polysaccharides, fungal-type cell wall biogenesis, cell wall mannoprotein biosynthesis, LPS/Lipid A pathways, and UDP-glucose metabolism), suggesting a shared role in assembling or remodeling glycans of the cell wall across diverse organisms.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019877","count":2},{"id":"GO:0045228","count":2},{"id":"GO:0019252","count":2},{"id":"GO:0009245","count":2},{"id":"GO:0045226","count":2}]},{"hash":"1645262477243045387","title":"ER stress response and ribophagy","description":"The cluster's prominent GO terms point to endoplasmic reticulum\u2013associated processes, including ribophagy, ER protein folding, and responses to ER stress, suggesting a focus on ER quality control and stress response pathways. Some transcription-regulation terms appear but are likely secondary to the core ER-related functions.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034517","count":2},{"id":"GO:0016032","count":2},{"id":"GO:0033158","count":1},{"id":"GO:0034976","count":1},{"id":"GO:0006662","count":1}]},{"hash":"972844274926379678","title":"Unknown","description":"The terms include cytosine metabolic process, amino acid biosynthesis (valine, methionine cycle), and stress/sporulation responses, with several obsolete GO terms. There is no clear single biological function connecting these proteins, and there are no interactions (Edges=0), suggesting annotation noise rather than a cohesive cluster.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0019858","count":2},{"id":"GO:0071361","count":2},{"id":"GO:0007584","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0030435","count":1}]},{"hash":"1938477074119854868","title":"Bacterial DNA replication and SOS response","description":"This cluster is driven by strong representation of DNA replication and SOS response terms (DNA replication, SOS response, DNA recombination), indicating a focus on bacterial DNA maintenance and damage repair pathways. A couple of terms relate to membrane transport in Gram-positive bacteria (teichoic acid transport, bacteriocin transport) and other processes, which appear as minor outliers rather than the core theme. Overall, the dominant theme is bacterial DNA replication and damage response.","confidence":"High","size":7,"edges":4,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0009432","count":3},{"id":"GO:0018144","count":3},{"id":"GO:0006310","count":2},{"id":"GO:0090394","count":2}]},{"hash":"351784940478705586","title":"Protein folding and signaling regulation","description":"The GO terms cluster around modulating signaling (negative regulation of kinase activity; regulation of synaptic potentiation) and maintaining protein homeostasis (chaperone-assisted refolding, post-translational targeting to membranes, regulation of heat response and inclusion body assembly), suggesting a theme of protein quality control coupled with signaling regulation. Some terms (karyogamy, DNA replication, angiogenesis) seem less directly connected and may be incidental. ","confidence":"Medium","size":7,"edges":15,"triangles":13,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000742","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0070389","count":2},{"id":"GO:0006260","count":2},{"id":"GO:1900035","count":2}]},{"hash":"2052649144771489641","title":"NF-kappaB\u2013driven immune signaling","description":"The cluster is dominated by GO terms for innate immune response and regulation of NF-kappaB transcription factor activity, plus B cell receptor signaling, suggesting a cohesive function in NF-kappaB\u2013mediated immune signaling that spans innate and adaptive immunity. Some terms related to development or microtubule localization are present but peripheral to the main theme.","confidence":"High","size":7,"edges":8,"triangles":5,"max_degree":4,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0051092","count":6},{"id":"GO:0045087","count":6},{"id":"GO:0035372","count":6},{"id":"GO:0016477","count":5},{"id":"GO:0010898","count":5}]},{"hash":"292127512610293802","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031146","count":2},{"id":"GO:0008285","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0061158","count":1},{"id":"GO:1903883","count":1}]},{"hash":"714820733338277603","title":"Ubiquitin-dependent protein regulation and turnover","description":"The top terms are dominated by ubiquitination-related processes (polyubiquitination, linear polyubiquitination, autoubiquitination) and ubiquitin-dependent protein catabolic processes, with linked regulatory roles in transcription by RNA Pol II, apoptosis/necroptosis, and histone turnover. This suggests a cohesive module where ubiquitin signaling governs protein stability and turnover and modulates signaling and cell fate pathways.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":3},{"id":"GO:0034121","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0043066","count":3},{"id":"GO:0000209","count":3}]},{"hash":"698647247770064119","title":"Heterochromatin formation and transcriptional silencing","description":"This cluster is dominated by GO terms related to chromatin organization and heterochromatin formation, including silent mating-type cassette heterochromatin formation, subtelomeric heterochromatin formation, DNA replication-dependent chromatin assembly, and negative regulation of chromosome condensation, plus transcriptional repression. While a few terms touch on development, the shared theme is chromatin silencing and telomeric/subtelomeric chromatin regulation.","confidence":"High","size":7,"edges":14,"triangles":13,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":7},{"id":"GO:1904815","count":5},{"id":"GO:0030466","count":5},{"id":"GO:0051290","count":5},{"id":"GO:1904693","count":5}]},{"hash":"741458745472043592","title":"Plant Hormone Signaling and Floral Development","description":"These terms point to hormone-regulated plant development, especially ABA and ethylene signaling, seed and floral meristem growth, and related transcriptional regulation. While stress-related responses like chitin signaling appear, the dominant theme is hormone-driven developmental processes in plants, including seeds and flowers.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009738","count":3},{"id":"GO:0060774","count":2},{"id":"GO:0048316","count":2},{"id":"GO:1901959","count":2},{"id":"GO:0009873","count":2}]},{"hash":"1906144540460362051","title":"Gasotransmitter signaling and redox metabolism","description":"The terms point to gasotransmitters like nitric oxide and hydrogen sulfide (NO-mediated signaling, guanylate cyclase regulation, H2S biosynthesis) and redox-related signaling (H2O2-mediated programmed cell death, nitrate catabolism) along with inflammatory and lipid mediator processes (interleukin-6 production, prostaglandin secretion, fatty acid oxidation). This suggests a functional cluster centered on redox signaling networks and gasotransmitter biology linked to lipid and cytokine signaling.","confidence":"Medium","size":7,"edges":17,"triangles":19,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0032770","count":1},{"id":"GO:1901206","count":1},{"id":"GO:0031284","count":1},{"id":"GO:0072604","count":1},{"id":"GO:0070814","count":1}]},{"hash":"548055213091014481","title":"Nucleolar transcription and ribosome biogenesis","description":"GO terms show strong emphasis on nucleolar rRNA transcription by RNA polymerase I, transcription by RNA polymerases II and III, and ribosome biogenesis, indicating a shared nuclear transcription/ribosome assembly function in the nucleolus. A few outliers (e.g., translesion synthesis) exist but do not alter the overall theme of transcription and ribosome production.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0042790","count":1},{"id":"GO:1904750","count":1},{"id":"GO:0001172","count":1},{"id":"GO:0042797","count":1}]},{"hash":"1917068656199077856","title":"Membrane transport of xenobiotics and lipids","description":"The top GO terms cluster around diverse transport activities across membranes and organelles (xenobiotic export, lipid/ceramide translocation, peroxisomal/mitochondrial transport, teichoic acid and bacteriocin transport), indicating proteins that facilitate movement of various substrates rather than a single substrate or pathway.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046618","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0015910","count":2},{"id":"GO:0015777","count":2},{"id":"GO:0043213","count":2}]},{"hash":"958814917525310980","title":"Calcium signaling in heart and neural plasticity","description":"The top terms include heart development and vascular morphogenesis, along with long-term potentiation and its regulation, and calcium-release into the cytosol plus guanylate cyclase activity. This suggests a common theme of calcium-dependent signaling influencing both cardiovascular development and neural synaptic plasticity, even though a few terms are obsolete or peripheral. Confidence: Medium","confidence":"","size":7,"edges":9,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0001569","count":1},{"id":"GO:1901841","count":1},{"id":"GO:1900271","count":1},{"id":"GO:0060291","count":1},{"id":"GO:0090151","count":1}]},{"hash":"683605996501391474","title":"Beta-lactam Antibiotic Catabolism & Response","description":"Dominant GO terms point to metabolism and response to beta-lactam antibiotics (beta-lactam antibiotic catabolic process, response to antibiotic) and regulation of beta-lactamase activity, with additional nylon catabolic process. Together these indicate a cluster of proteins involved in antibiotic degradation and modulation of antibiotic resistance enzymes, rather than a single coherent cellular process. The presence of a few unrelated terms likely reflects annotation noise rather than a shared function.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030655","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0019876","count":5},{"id":"GO:0033252","count":5},{"id":"GO:0016477","count":1}]},{"hash":"536442968979263631","title":"Sodium and Proton Ion Transporters","description":"The cluster is defined by GO terms for sodium ion transmembrane transport and proton transmembrane transport, suggesting a shared role as membrane ion transporters (Na+ and H+). With only these two related terms and no observed interactions, the label centers on their common transporter function.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035725","count":1},{"id":"GO:0015992","count":1}]},{"hash":"735006533577903467","title":"Stress-responsive kinase signaling and transcription","description":"The cluster's GO terms prominently feature kinase activity (protein autophosphorylation; positive regulation of serine/threonine kinase activity) and transcription regulation, plus a xenobiotic stress response and plant hormone signaling elements. This pattern suggests a group of proteins that transmit signals via phosphorylation to control gene expression under stress, rather than a single enzymatic function.","confidence":"Medium","size":7,"edges":8,"triangles":2,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006261","count":1},{"id":"GO:0071902","count":1},{"id":"GO:0035690","count":1},{"id":"GO:0017006","count":1},{"id":"GO:0032092","count":1}]},{"hash":"1685576713385978245","title":"Lysosome trafficking and autophagy","description":"The top GO terms converge on lysosomal targeting and endomembrane trafficking (Golgi to lysosome transport, protein targeting to lysosome, endomembrane system organization) and autophagic degradation (aggrephagy), suggesting a cohesive role in lysosome-directed trafficking and autophagy. Cytoskeletal/membrane signaling terms (filopodium/microspike assembly, PI5P metabolism) may reflect supporting roles in trafficking dynamics, while a few immune signaling terms add context but do not redefine the main theme. ","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090160","count":1},{"id":"GO:0034145","count":1},{"id":"GO:0048549","count":1},{"id":"GO:1904562","count":1},{"id":"GO:0030035","count":1}]},{"hash":"29773270524134032","title":"Mitochondrial Transport and Membrane Potential Regulation","description":"The top GO terms point strongly to mitochondrial processes, especially regulation of mitochondrial membrane permeability and membrane potential, along with transport across mitochondrial membranes such as ADP, ATP, and alpha-ketoglutarate transport, plus related metabolic and redox responses. This suggests the cluster reflects mitochondrial energetics and metabolite transport rather than a broader, non-mitochondrial function. The presence of insulin-related stimulus terms may indicate metabolic regulation linked to mitochondria, but the dominant theme remains mitochondrial transport and membrane regulation.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":1},{"id":"GO:0051881","count":1},{"id":"GO:0015742","count":1},{"id":"GO:0032869","count":1},{"id":"GO:1990314","count":1}]},{"hash":"2096781907615612349","title":"Trehalose and glucosylglycerol biosynthesis under stress","description":"This cluster is enriched for trehalose biosynthetic process and glucosylglycerol biosynthesis, with associated stress responses (heat, desiccation, toxic substances). The common theme is production of compatible solutes to protect cells under stress.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0070415","count":1},{"id":"GO:0034605","count":1},{"id":"GO:0090441","count":1}]},{"hash":"618458259118122117","title":"Neural development and ER\u2013mitochondria stress response","description":"Many top GO terms point to neural development (substantia nigra development; neural precursor proliferation; regulation of dendritic spine morphogenesis) and cellular stress/ER-mitochondria interplay (response to endoplasmic reticulum stress, mitochondrion\u2013ER tethering, redox homeostasis). This pattern suggests a cluster centered on neuronal development coordinated with ER\u2013mitochondria signaling and oxidative stress management, rather than a single broad process.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0034976","count":3},{"id":"GO:1903206","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0021762","count":3},{"id":"GO:0045453","count":3}]},{"hash":"2039980705872006986","title":"Skeletal mineralization and vitamin D response","description":"The presence of endochondral ossification and cementum mineralization strongly points to bone/mineralization biology; the vitamin D response term supports a link to calcium-bone metabolism. Other GO terms (plant phototropism, aromatic compound degradation) may be less informative or represent broad annotations.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0042952","count":2},{"id":"GO:0009636","count":2},{"id":"GO:0009820","count":2}]},{"hash":"1117084179247460073","title":"Unknown","description":"The top GO terms are a mixed bag (brain segmentation, seedling development, immune encapsulation, protein glycosylation) with many obsolete annotations, offering no cohesive biological function or pathway to unite the cluster. Therefore a single interpretable label cannot be assigned.","confidence":"","size":7,"edges":10,"triangles":3,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006049","count":1},{"id":"GO:0035010","count":1},{"id":"GO:0035284","count":1},{"id":"GO:0006486","count":1},{"id":"GO:0090351","count":1}]},{"hash":"615976713249835882","title":"Unknown","description":"The terms are highly diverse, spanning translation and ribosome maturation, protein oligomerization, cytoskeletal stress fiber assembly, and neuronal/ion-channel related processes like synaptic depression, magnesium response, membrane hyperpolarization, and mechanosensory pain detection. With no edges or clear functional linkage among these terms, there is no cohesive theme to define a specific cluster label.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006417","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0000470","count":1},{"id":"GO:0051260","count":1},{"id":"GO:1900454","count":1}]},{"hash":"1353996413109673796","title":"RNA processing and ribosome biogenesis","description":"Dominated by RNA-related terms: RNA catabolic process, RNA phosphodiester bond hydrolysis (endonucleolytic), and ribonucleotide excision repair, with a single entry linked to ribosome biogenesis. This pattern points to a functional group focused on RNA metabolism and ribosome assembly/maintenance, with a possible plastid-related context and minor unrelated terms that may reflect annotation noise.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0090502","count":3},{"id":"GO:1990516","count":3},{"id":"GO:0006401","count":3},{"id":"GO:0042254","count":1},{"id":"GO:0032147","count":1}]},{"hash":"1866546927875485285","title":"Ciliary movement and neuronal vesicle transport","description":"The cluster is dominated by GO terms for cilium movement (GO:0003341) and anterograde neuronal dense core vesicle transport (GO:1990048), pointing to microtubule-based movement and vesicle trafficking in cilia and neurons. Other terms related to DNA replication and chromatin are present but appear less central, suggesting some annotation noise or multi-functional proteins; however, the core theme centers on movement/transport along cellular networks.","confidence":"Medium","size":7,"edges":8,"triangles":3,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0003341","count":6},{"id":"GO:1990048","count":6},{"id":"GO:0030466","count":5},{"id":"GO:0006260","count":5},{"id":"GO:0006279","count":5}]},{"hash":"486316148877762283","title":"Angiogenesis and endothelial cell migration","description":"The cluster shows strong enrichment for angiogenesis and endothelial cell migration terms (GO:0001525, GO:0016477), indicating a vascular development theme. Related development terms (lung-associated mesenchyme development) support a developmental context, while accompanying DNA replication/repair and stress-related terms likely reflect proliferative and stress-responsive states in angiogenic endothelial cells. Overall, the main signal centers on vascular formation and endothelial movement, with supporting genome maintenance and stress-response processes.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0007100","count":3},{"id":"GO:0043536","count":3},{"id":"GO:0001525","count":3},{"id":"GO:0006281","count":3}]},{"hash":"1268416577653992593","title":"Developmental cell cycle and morphogenesis","description":"This cluster is dominated by GO terms for DNA replication and centrosome cycle, pointing to cell cycle regulation, alongside developmental/morphogenetic terms such as embryonic cranial skeleton morphogenesis and corpus callosum development. Additional links to cell migration and apoptotic regulation fit into a broader developmental context, with a few terms (e.g., B cell receptor signaling) less aligned. Overall, the shared theme centers on developmental processes coupled with cell cycle control.","confidence":"Medium","size":7,"edges":10,"triangles":2,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0010571","count":7},{"id":"GO:0006260","count":7},{"id":"GO:0007098","count":7},{"id":"GO:0048701","count":7},{"id":"GO:0016477","count":6}]},{"hash":"1930925872288968908","title":"Keratinocyte differentiation and growth signaling","description":"Keratinocyte differentiation is among the top terms, and the cluster highlights core growth-regulating pathways, notably canonical Wnt signaling and Hippo signaling, which govern epithelial proliferation, differentiation, and cell migration. While other terms touch on broader processes like apoptosis and mitosis, the strongest shared theme is epithelial growth control and cell fate decisions mediated by Wnt/Hippo networks.","confidence":"High","size":7,"edges":10,"triangles":5,"max_degree":6,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060044","count":5},{"id":"GO:0030216","count":5},{"id":"GO:0090263","count":5},{"id":"GO:0035329","count":5},{"id":"GO:0007601","count":5}]},{"hash":"587893235269682822","title":"Membrane lipid metabolism and metal ion transport","description":"Top GO terms show lipid-processing activities (lipid glycosylation, phospholipid dephosphorylation, lipopolysaccharide biosynthesis) alongside transport of metal ions (zinc, copper, cadmium) and lipid-associated pathways (epoxygenase P450 pathway). This mix points to a functional theme at the membrane involving lipid metabolism and metal ion transport, hence the label.","confidence":"Medium","size":7,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016999","count":2},{"id":"GO:0030259","count":2},{"id":"GO:0071577","count":2},{"id":"GO:0006825","count":2},{"id":"GO:0019373","count":2}]},{"hash":"110383736814979966","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"carbohydrate metabolic process","top_go_terms":[{"id":"GO:0046380","count":3},{"id":"GO:0046839","count":3},{"id":"GO:0032361","count":3},{"id":"GO:0097755","count":3},{"id":"GO:0006045","count":3}]},{"hash":"446422095390930821","title":"Lipid biosynthesis and cell wall metabolism","description":"The top GO terms point to lipid biosynthetic and lipid-related metabolic processes (lipid A biosynthesis, lipid X metabolism, phylloquinone biosynthesis) as well as various cell wall\u2013associated processes (cell wall macromolecule catabolic process, cell wall organization), with additional catabolic and biosynthetic activities. This suggests a cluster involved in both lipid metabolism and cell wall remodeling or turnover, hence the combined label.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0009245","count":1},{"id":"GO:2001289","count":1},{"id":"GO:0009063","count":1},{"id":"GO:0019394","count":1}]},{"hash":"107598378254782804","title":"Steroid Hormone Metabolism","description":"This cluster is driven by androgen metabolic and catabolic processes and glucocorticoid biosynthesis, which together point to a steroid hormone metabolism theme. Other terms (transcription regulation, lung development, various biosynthetic/catabolic processes) appear as less cohesive background signals, suggesting some heterogeneity, but the steroid-related processes are the strongest shared function among the proteins.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0046677","count":3},{"id":"GO:0008209","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006710","count":2}]},{"hash":"1787273027645871217","title":"Purine degradation with allantoin/ureide catabolism","description":"The top GO terms are dominated by purine-related catabolic processes (purine nucleobase catabolic process, allantoin catabolic process, ureide catabolic process), suggesting a shared function in degrading nitrogen-containing metabolites. While there are a few terms related to antibiotic biosynthesis and other biosynthetic processes, these are less representative of the main theme; thus, the cluster most plausibly reflects purine/ureide catabolism.","confidence":"Medium","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0018401","count":1},{"id":"GO:0055114","count":1},{"id":"GO:1901874","count":1},{"id":"GO:0032364","count":1}]},{"hash":"876033153193828121","title":"Vasculogenesis and myoblast differentiation regulation","description":"The top terms point to developmentally coordinated signaling: positive regulation of vasculogenesis and positive regulation of myoblast differentiation, with a related note on Notch signaling regulation. Although several obsolete or broad terms (e.g., transcription and hydroxylation notes) appear, the strongest, coherent theme is regulation of vascular and muscle lineage development. This suggests the cluster captures regulators of developmental signaling affecting blood vessel formation and muscle cell differentiation.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2001214","count":2},{"id":"GO:0061428","count":2},{"id":"GO:0045746","count":2},{"id":"GO:0042264","count":2},{"id":"GO:0042265","count":2}]},{"hash":"292023882855518738","title":"Androgen signaling and prostate development","description":"The top GO terms cluster around male sex differentiation, prostate gland development, and steroid hormone receptor complex assembly, indicating a core role in androgen signaling and prostate development. Additional terms like cellular response to type I interferon and unfolded protein response suggest auxiliary stress-related regulation, but the dominant pattern supports androgen receptor\u2013driven/prostate-associated functions.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0046661","count":6},{"id":"GO:0071357","count":6},{"id":"GO:0006463","count":6},{"id":"GO:0030850","count":6},{"id":"GO:0051348","count":5}]},{"hash":"318173056504497558","title":"Steroid and lipid biosynthesis","description":"Based on the top GO terms, multiple entries point to lipid and steroid metabolism, including androgen metabolic process, androgen catabolic process, glucocorticoid biosynthetic process, fatty acid elongation, and mycolic acid biosynthetic process. Acetoin catabolic process adds a general metabolism signal, while lung development and melanin biosynthesis suggest broader biosynthetic roles. The strongest common theme across terms is lipid- and steroid-related biosynthesis/metabolism, so this label best captures the cluster's functional signal. ","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0006355","count":5},{"id":"GO:0055114","count":5},{"id":"GO:0008209","count":4},{"id":"GO:0006710","count":4},{"id":"GO:0030324","count":4}]},{"hash":"1544504883191542850","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009718","count":3},{"id":"GO:0042351","count":3},{"id":"GO:0080110","count":3},{"id":"GO:0042619","count":3},{"id":"GO:0009244","count":3}]},{"hash":"467064816323012162","title":"Ubiquitin-dependent innate immune signaling regulators","description":"The Top Terms cluster around ubiquitination processes (autoubiquitination, ERAD-associated ubiquitination, and K63-linked polyubiquitination) and regulation of signaling pathways. There is emphasis on NF-kappaB signaling, TLR pathway regulation, and broader control of transcription, apoptosis, necroptosis, and cell cycle. This suggests proteins that modulate immune signaling and cell fate through ubiquitin modification.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0043123","count":3},{"id":"GO:0000122","count":2}]},{"hash":"896481159575878230","title":"Platelet\u2013Leukocyte Activation and Lectin Signaling","description":"The terms cluster around activation and signaling in platelets and leukocytes (platelet activation, basophil activation, Fc-gamma receptor signaling, C-type lectin receptor signaling, leukocyte tethering/rolling) and innate inflammatory pathways (arachidonate secretion, complement activation via the lectin pathway). This suggests a cohesive theme of immune cell activation and interaction mediated by platelet and lectin/fc-receptor signaling, with vascular/trafficking components supporting inflammation.","confidence":"High","size":7,"edges":11,"triangles":7,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0010572","count":5},{"id":"GO:2000502","count":4},{"id":"GO:0038094","count":4},{"id":"GO:0036303","count":4},{"id":"GO:0090238","count":4}]},{"hash":"1877215782854181239","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030154","count":1},{"id":"GO:0048477","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0071039","count":1}]},{"hash":"596222988238016372","title":"Unknown","description":"Top terms span both nuclear processes (translation, CENP-A chromatin assembly, chromatid cohesion) and secretory pathway activities (ER-Golgi transport, ERAD, retrograde transport) plus stress responses, with no single unifying function and no edges linking members. This makes it unclear to assign a coherent biological theme, so the label is Unknown with None confidence. ","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0007064","count":3},{"id":"GO:0046677","count":2},{"id":"GO:0006888","count":2},{"id":"GO:0060416","count":2}]},{"hash":"2153491447844723862","title":"Neuronal Ion Transport and Membrane Potential","description":"This cluster is dominated by GO terms for ion transport (potassium, sodium, calcium), membrane hyperpolarization, and intracellular potassium homeostasis, plus a pain perception term, pointing to proteins that regulate membrane potential and excitability in neurons or other excitable cells. Some development and metabolic regulation terms appear but do not override the core neural/ion-transport theme.","confidence":"Medium","size":7,"edges":18,"triangles":22,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0060081","count":4},{"id":"GO:0071805","count":4},{"id":"GO:0097623","count":4},{"id":"GO:0030007","count":4},{"id":"GO:0098719","count":4}]},{"hash":"1703122672709599256","title":"Retroviral assembly and integration","description":"This cluster's terms cluster around retroviral life-cycle steps\u2014virion assembly, ESCRT-mediated budding, DNA integration, and proviral latency\u2014indicating a cohesive theme of retroviral replication and latency. Some RNA-processing and apoptosis-related terms likely reflect host\u2013virus interaction dynamics, but the dominant signals point to retroviral processes.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0039702","count":1},{"id":"GO:0015074","count":1},{"id":"GO:0019068","count":1},{"id":"GO:0000398","count":1},{"id":"GO:0072756","count":1}]},{"hash":"1837248618709140516","title":"Viral infection and host interaction","description":"The GO terms cluster around virion assembly, viral life cycle, and host-related processes (e.g., leukocyte migration, host-mediated activation of viral genome replication), suggesting these proteins are linked to virus-host interactions and replication. Some outliers (sepal formation, oxidative phosphorylation regulation) likely reflect annotation noise, but the dominant signal points to viral infection processes, justifying the label. ","confidence":"Medium","size":7,"edges":5,"triangles":0,"max_degree":5,"top_function":"protein folding","top_go_terms":[{"id":"GO:2000276","count":7},{"id":"GO:0019068","count":7},{"id":"GO:0048453","count":7},{"id":"GO:0075713","count":7},{"id":"GO:0006457","count":7}]},{"hash":"1177763934550528131","title":"Pseudouridine Synthesis and Ribosome Biogenesis","description":"This cluster is driven by GO terms for tRNA and rRNA pseudouridine synthesis, tRNA modification, and ribosome biogenesis with export of the large subunit, pointing to a shared role in RNA modification and ribosome assembly/translation. Some cell cycle-related terms appear but are likely secondary to the dominant RNA-processing theme.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031119","count":2},{"id":"GO:0000455","count":2},{"id":"GO:0006400","count":2},{"id":"GO:0042254","count":1},{"id":"GO:0000055","count":1}]},{"hash":"937441178767105759","title":"Heat stress and protein folding cluster","description":"Most represented GO terms center on cellular stress response and protein quality control: response to heat, response to unfolded protein, and protein folding in the endoplasmic reticulum. This points to a theme of heat-shock / chaperone-mediated protein folding, despite a few outlier terms like pyrroloquinoline quinone biosynthesis and DNA replication. Confidence: Medium","confidence":"","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0018189","count":2},{"id":"GO:0009408","count":1},{"id":"GO:0006260","count":1},{"id":"GO:1900035","count":1},{"id":"GO:1901621","count":1}]},{"hash":"1255189831609058450","title":"Mitochondrial respiration and proton transport","description":"Rationale: The top GO terms\u2014aerobic respiration, mitochondrial electron transport (ubiquinol to cytochrome c), and proton transmembrane transport\u2014point to proteins functioning in the mitochondrial electron transport chain and proton pumping, i.e., oxidative phosphorylation. The theme is coherent across terms, supporting this label, though the modest term counts suggest a medium level of confidence.","confidence":"Medium","size":7,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":1},{"id":"GO:0006122","count":1},{"id":"GO:1902600","count":1}]},{"hash":"2302334676993671147","title":"Unknown","description":"The top GO terms include phytochelatin and plastoquinone biosynthesis, ozone response, and a variety of regulatory processes, which do not point to a single cohesive function or pathway across the proteins. There are no edges to suggest a shared interaction, so no clear theme emerges; label as Unknown with None.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046938","count":1},{"id":"GO:1904715","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0043085","count":1},{"id":"GO:0010193","count":1}]},{"hash":"1949593618621241862","title":"Mitochondrial Transport and Membrane Regulation","description":"This cluster centers on mitochondrial function, with GO terms emphasizing transport of metabolites and ions (ADP, ATP, alpha-ketoglutarate, magnesium), and regulation of mitochondrial membrane permeability and membrane potential. The inclusion of insulin and IGF responses suggests metabolic signaling linked to mitochondrial activity, plus a oxidative stress response theme. Together, these terms point to mitochondria-centric transport and membrane regulation as the core function of the group.","confidence":"High","size":7,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":4},{"id":"GO:0051881","count":4},{"id":"GO:0015742","count":4},{"id":"GO:0032869","count":4},{"id":"GO:1990314","count":4}]},{"hash":"684536079384225992","title":"Cholesterol Metabolism and Cellular Response","description":"The cluster is dominated by cholesterol-related terms: cholesterol biosynthetic process, cholesterol metabolic process, and cellular response to cholesterol, with a note on positive regulation of cholesterol efflux. A few development/neural terms appear as outliers, but the core theme is cholesterol metabolism and response.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":2},{"id":"GO:0008542","count":2},{"id":"GO:0021522","count":1},{"id":"GO:0010875","count":1},{"id":"GO:0071397","count":1}]},{"hash":"134455241837937195","title":"Mitochondrial transport and membrane energetics","description":"The top GO terms cluster around mitochondrial function: regulation of membrane permeability and potential, transport of metabolites (ADP, ATP, alpha-ketoglutarate), and ion handling (Mg2+), along with a response to oxidative stress and insulin/IGF signaling. This suggests a coherent module of mitochondrial metabolite transport coupled to the maintenance of mitochondrial energetics and signaling, rather than a broader non-mitochondrial process.","confidence":"High","size":7,"edges":7,"triangles":1,"max_degree":6,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":4},{"id":"GO:0051881","count":4},{"id":"GO:0015742","count":4},{"id":"GO:0032869","count":4},{"id":"GO:1990314","count":4}]},{"hash":"1755589321425386309","title":"GPCR-Driven Signaling Network","description":"This cluster is best described by GPCR-driven signaling, given the prominence of GO terms for GPCR pathways that activate adenylate cyclase and phospholipase C (e.g., GO:0007190, GO:0007189, GO:0007200). Additional terms point to hormone signaling (thyroid-stimulating hormone), neural context (regulation of axonogenesis), and immune defense (defense response to virus, toll-like receptor 8 signaling), suggesting GPCR signaling intersects with endocrine, neural, and immune processes. The combination implies a network of GPCR-mediated signaling with cross-talk to immune and neuroendocrine functions, rather than a single, narrow pathway. ","confidence":"High","size":7,"edges":12,"triangles":8,"max_degree":6,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0034158","count":7},{"id":"GO:0060408","count":7},{"id":"GO:0007190","count":7},{"id":"GO:0007200","count":7},{"id":"GO:0009992","count":7}]},{"hash":"1420186250494414982","title":"TLR Signaling and Interferon Production","description":"GO terms cluster around TLR signaling (TLR8/9) and interferon production, indicating innate immune sensing and cytokine responses in dendritic cells, with slight noise from a few unrelated plant/bone terms.","confidence":"High","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0009620","count":3},{"id":"GO:0045359","count":3},{"id":"GO:0034162","count":3},{"id":"GO:0010080","count":3},{"id":"GO:1900155","count":3}]},{"hash":"355575032019148763","title":"Developmental morphogenesis and cytoskeletal regulation","description":"This cluster has several development-related terms (forebrain development, skeletal system morphogenesis) and processes tied to cytoskeletal dynamics (Arp2/3 complex-mediated actin nucleation). Additional terms point to growth control and proteostasis (SCF ubiquitin-dependent degradation, regulation of G0 to G1 transition), suggesting a broader theme of development coupled with cytoskeletal remodeling and cell-cycle control. Some terms are peripheral (mRNA branch site recognition, GCN2 signaling), but the dominant pattern supports a developmental and cytoskeletal/growth regulatory theme.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":3},{"id":"GO:0048705","count":2},{"id":"GO:0031146","count":2},{"id":"GO:0070317","count":2},{"id":"GO:0030900","count":2}]},{"hash":"1206937358086361517","title":"Anaerobic metabolism and fermentation","description":"The top GO terms point to metabolic processes dominated by anaerobic energy pathways (methanogenesis, anaerobic amino-acid fermentation) alongside general metabolism (acyl-CoA, redox, and pteridine-containing compound metabolism). A few terms appear obsolete or outliers (e.g., post-embryonic development), suggesting a loosely connected set of metabolism-related proteins with emphasis on anaerobic/fermentative functions. ","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009086","count":2},{"id":"GO:0019670","count":2},{"id":"GO:0006637","count":2},{"id":"GO:0009791","count":2},{"id":"GO:0015948","count":2}]},{"hash":"1531866864148878712","title":"Neural development and axon guidance","description":"The top GO terms are dominated by neuronal development and axon guidance processes (positive regulation of synapse assembly, optic nerve morphogenesis, retinal ganglion cell axon guidance, corpus callosum development), suggesting the cluster represents genes involved in neural development and axon pathfinding. Some other terms appear in the list but do not override the clear neuronal theme. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0051965","count":6},{"id":"GO:0022038","count":6},{"id":"GO:0033628","count":6},{"id":"GO:0021631","count":6},{"id":"GO:0050798","count":6}]},{"hash":"986327978974887023","title":"ER Stress\u2013Linked Transcription Regulation","description":"This cluster is enriched for GO terms tying transcriptional regulation (DNA-templated transcription, transcription factor activity, DNA binding) to nuclear processes, alongside ER-associated functions (response to ER stress, protein folding in ER). The inclusion of negative regulation of transcription by RNA polymerase II and nuclear import/export regulation suggests coordination between nuclear transcription control and ER stress responses. Overall, the proteins likely participate in linking transcription regulation with ER protein processing and stress responses.","confidence":"Medium","size":7,"edges":4,"triangles":0,"max_degree":3,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0006351","count":5},{"id":"GO:0046826","count":5},{"id":"GO:0033158","count":3},{"id":"GO:0034976","count":3},{"id":"GO:0006662","count":3}]},{"hash":"152323415356972787","title":"Viral life cycle and host interaction","description":"The top GO terms are dominated by viral-related processes (virion assembly, viral life cycle, host-mediated activation of viral genome replication, viral release from host, establishment of integrated proviral latency, symbiont entry into host), indicating the cluster centers on viral replication and host interaction. A few terms like protein folding and sepal formation appear as low-frequency outliers, but they do not define the cluster\u2019s main theme. This makes \"Viral life cycle and host interaction\" a concise, representative label with strong confidence.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000276","count":1},{"id":"GO:0019068","count":1},{"id":"GO:0048453","count":1},{"id":"GO:0075713","count":1},{"id":"GO:0006457","count":1}]},{"hash":"1305740954416174336","title":"Viral infection and replication","description":"The terms predominantly point to stages of the viral life cycle (virion assembly, viral life cycle, viral release, proviral latency) and host\u2013virus interactions (host-mediated activation of viral genome replication, entry into host), with a single non-viral term present. This supports labeling the cluster as Viral infection and replication.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:2000276","count":1},{"id":"GO:0019068","count":1},{"id":"GO:0048453","count":1},{"id":"GO:0075713","count":1},{"id":"GO:0006457","count":1}]},{"hash":"1045070193038391314","title":"TLR signaling and innate immunity","description":"The top GO terms are dominated by Toll-like receptor signaling pathways (TLR6, TLR8, TLR9) and related innate immune responses (Toll signaling pathway, response to fungus, response to diacyl lipopeptide). Although there are a few neural development terms in the set, the strongest and most coherent signal is Toll-like receptor\u2013mediated innate immunity, supporting a label centered on TLR signaling. ","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":"inflammatory response","top_go_terms":[{"id":"GO:0009620","count":3},{"id":"GO:0071726","count":3},{"id":"GO:0034162","count":3},{"id":"GO:0051965","count":3},{"id":"GO:1902499","count":3}]},{"hash":"36092107528895492","title":"Unknown","description":"The listed GO terms are highly diverse, spanning behavioral responses, cell adhesion, immune signaling, hypoxia response, insulin regulation, and host-symbiont interactions, with no single coherent function tying the proteins together. Because there isn\u2019t a clear, common theme, a concise, representative label cannot be confidently derived.","confidence":"","size":7,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0035641","count":1},{"id":"GO:0060244","count":1},{"id":"GO:0001662","count":1},{"id":"GO:0008284","count":1},{"id":"GO:0001666","count":1}]},{"hash":"931397064012062114","title":"Unknown","description":"The GO terms span several unrelated areas (cobalamin biosynthesis, sporulation, embryo axis development, pheromone maturation, and LDL receptor\u2013related processes). There is no single, coherent function that connects these terms, so a meaningful functional label cannot be assigned.","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":3},{"id":"GO:1905596","count":2},{"id":"GO:0030435","count":2},{"id":"GO:0090472","count":2},{"id":"GO:0007354","count":2}]},{"hash":"1242130326135052","title":"Unknown","description":"The terms are highly diverse (mRNA decay, lipid and carbohydrate metabolism, cellulose/xylan degradation, pantothenate biosynthesis, and mitochondrial fusion regulation) with no clear single function tying the proteins together. ","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000184","count":1},{"id":"GO:0032508","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0000271","count":1},{"id":"GO:0046168","count":1}]},{"hash":"688742851390067607","title":"Calcium-Activated Phospholipid Scrambling","description":"The top GO terms cluster around calcium-activated scrambling of phospholipids (PS and PC), bleb assembly, and links to coagulation and phagocytosis, with supporting roles in purinergic signaling and ion transport. This suggests the proteins participate in calcium-dependent membrane remodeling and signaling that governs lipid exposure and related surface processes.","confidence":"Medium","size":7,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045794","count":1},{"id":"GO:0035590","count":1},{"id":"GO:0061590","count":1},{"id":"GO:0061589","count":1},{"id":"GO:0007596","count":1}]},{"hash":"1046573133422388053","title":"Embryonic Morphogenesis and Tissue Patterning","description":"Several top GO terms point to embryonic development and tissue formation, including mesoderm development, cartilage morphogenesis, endocardial epithelial-to-mesenchymal transition, left-right patterning, palate development, placental-related differentiation, and hair follicle morphogenesis. These consistently indicate a theme of developmental morphogenesis and lineage differentiation, rather than a single specific molecular function; the vitamin D biosynthesis regulation term appears peripheral. Overall, the cluster seems centered on early developmental patterning and organogenesis.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0003198","count":1},{"id":"GO:0031069","count":1},{"id":"GO:0060972","count":1},{"id":"GO:0060536","count":1},{"id":"GO:0060707","count":1}]},{"hash":"1584750417471940959","title":"Ribosome Biogenesis and Translational Machinery","description":"The cluster is dominated by GO terms tied to ribosome biogenesis, ribosomal subunit assembly, cytoplasmic translation, and tRNA aminoacylation, indicating a core role in protein synthesis and ribosome function. A small subset of terms (e.g., transcription by RNA Pol II and interleukin-4 response) appear as potential outliers, but overall the theme centers on translation and ribosome-related processes.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000027","count":1},{"id":"GO:0071353","count":1},{"id":"GO:0006614","count":1},{"id":"GO:0002181","count":1}]},{"hash":"205908236619651486","title":"Unknown","description":"Unknown","confidence":"","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035010","count":1},{"id":"GO:0006486","count":1},{"id":"GO:0006517","count":1},{"id":"GO:0016063","count":1},{"id":"GO:0006013","count":1}]},{"hash":"1106944986744891182","title":"Chemokine-mediated inflammatory signaling","description":"The cluster is dominated by terms related to chemokine production (e.g., CCL5, MIP-1\u03b1) and inflammatory signaling, with related hints at cell migration and immune communication, supporting a shared immune-response function.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086070","count":1},{"id":"GO:1903444","count":1},{"id":"GO:0016477","count":1},{"id":"GO:0007253","count":1},{"id":"GO:0072660","count":1}]},{"hash":"519619182710779142","title":"TLR-Mediated Innate Immune Signaling","description":"The dominant GO terms point to Toll-like receptor signaling (TLR8/9), Toll signaling, dendritic cell cytokine regulation, and interferon production (IFN-\u03b2 and type II IFN), with a fungal response context. This indicates a coherent module of innate immune sensing and interferon-mediated responses, despite a couple of unrelated terms in the list.","confidence":"High","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009620","count":1},{"id":"GO:0045359","count":1},{"id":"GO:0034162","count":1},{"id":"GO:0010080","count":1},{"id":"GO:1900155","count":1}]},{"hash":"993456871574074187","title":"Small Molecule Metabolic Processes","description":"The top GO terms span biosynthesis (biotin and antibiotics), catabolic steps (triglycerides, uracil, 1,2-dichloroethane), redox-related detoxification, and even a regulatory signaling term. Although there isn\u2019t a single specific pathway, they collectively reflect metabolism and processing of diverse small molecules, so a broad metabolic label is most representative.","confidence":"Medium","size":7,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":3},{"id":"GO:0017000","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0098869","count":3},{"id":"GO:2000124","count":3}]},{"hash":"851909439674953310","title":"Translation and ribosome maturation","description":"The top GO terms are dominated by translation (GO:0006412) with four proteins, along with ribosome biogenesis elements such as maturation of SSU-rRNA (GO:0000462) and trans-translation (GO:0070929). This pattern indicates a cluster centered on protein synthesis and ribosome maintenance, including ribosomal RNA processing and quality-control translation. A few other terms (e.g., protein modification, cell polarity, junction organization) are sporadic and likely represent peripheral annotations rather than core cluster functions.","confidence":"High","size":6,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":4},{"id":"GO:0000462","count":2},{"id":"GO:0070929","count":1},{"id":"GO:0031365","count":1},{"id":"GO:0043686","count":1}]},{"hash":"2112010152166354820","title":"Ubiquitin-Proteasome\u2013Mediated Cell Cycle Proteolysis","description":"Top GO terms cluster around ubiquitination and proteasomal degradation (APC/C- and SCF-dependent), including K11-linked ubiquitination and autoubiquitination, with ancillary hints at ERAD and histone turnover. This pattern supports a theme of proteolysis regulating cell cycle progression, i.e., proteins in this cluster likely participate in ubiquitin-mediated proteolysis during cell division. Some terms like splicing or TNF signaling may reflect broader regulatory connections or annotation noise.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031145","count":3},{"id":"GO:0051301","count":2},{"id":"GO:0070979","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0033209","count":2}]},{"hash":"1958215723925283281","title":"Microtubule dynamics and spindle assembly","description":"The terms cluster around microtubule-based processes: plus-end depolymerization, regulation of microtubule-based processes, spindle midzone assembly, and plus-end-directed vesicle transport along microtubules, as well as actomyosin ring assembly related to cytokinesis and metaphase chromosome handling. A plant-specific term for chloroplast movement fits the broader theme of cytoskeletal movement. Together these indicate a cohesive role in cytoskeletal dynamics during mitosis and intracellular transport, justifying the label.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0032487","count":6},{"id":"GO:0001560","count":6},{"id":"GO:0070462","count":6},{"id":"GO:0009904","count":6},{"id":"GO:1990942","count":6}]},{"hash":"891273289804250815","title":"Ubiquitin-Driven Regulation of Cell Cycle and Transcription","description":"The cluster centers on ubiquitin-related processes (polyubiquitination and ubiquitin-dependent degradation) and key regulatory activities such as cell cycle control, transcriptional repression, and apoptosis regulation, suggesting a cohesive theme of ubiquitin-mediated control of cell fate and gene expression.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000209","count":3},{"id":"GO:0071157","count":3},{"id":"GO:0000122","count":3},{"id":"GO:0043066","count":3},{"id":"GO:0007275","count":2}]},{"hash":"1437693206657673950","title":"Ribosome Biogenesis and Translation","description":"This cluster centers on translation and ribosome-related processes: translation, ribosome biogenesis, and RNA modification such as rRNA pseudouridine synthesis, indicating proteins involved in ribosome assembly and translational fidelity. The presence of mitochondrial translational termination suggests some overlap with organellar translation, while a few terms related to transcription/ RNA processing hint at broader RNA metabolism context. Overall, the dominant theme is ribosome function and protein synthesis.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0070126","count":2},{"id":"GO:0009236","count":1},{"id":"GO:0006461","count":1},{"id":"GO:0042254","count":1}]},{"hash":"249275389584034089","title":"Unknown","description":"The top GO terms are a mix of signaling regulation, development, and organellar processes with no clear shared function or organism-specific context, and there are no edges connecting the proteins. Therefore no cohesive label can be assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030512","count":1},{"id":"GO:0035970","count":1},{"id":"GO:0071560","count":1},{"id":"GO:0046827","count":1},{"id":"GO:0042006","count":1}]},{"hash":"2102746063050143886","title":"Unknown","description":"The terms are highly heterogeneous, ranging from hydrocarbon degradation (carbazole, toluene catabolic), photosynthesis and light harvesting (photosynthesis, nonphotochemical quenching), to diverse metabolic and membrane-related processes (CMP-N-acetylneuraminate metabolism, ergosterol and sphingolipid metabolism, proton transport, sebaceous gland differentiation). There isn\u2019t a single coherent function tying these six proteins together, so there is no clear representative label beyond Unknown.","confidence":"","size":6,"edges":6,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0046232","count":1},{"id":"GO:0042203","count":1},{"id":"GO:0010196","count":1},{"id":"GO:0015979","count":1}]},{"hash":"200263880005038426","title":"Antibiotic and Xenobiotic Transport","description":"The Top Terms point to export and transport of xenobiotics and related compounds (xenobiotic export, teichoic acid transport, bacteriocin transport/immunity, oligopeptide export from mitochondrion, long-chain fatty acid import into peroxisome, ceramide translocation) and an antibiotic response, suggesting a theme of membrane-associated transport and antimicrobial handling. Additional terms like cytochrome complex assembly and nucleotide-excision repair are less directly linked, so the overall signal supports a transport/antibiotic-response cluster with moderate confidence.","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0017004","count":5},{"id":"GO:0046677","count":5},{"id":"GO:0046618","count":4},{"id":"GO:0006289","count":4},{"id":"GO:0015910","count":4}]},{"hash":"347912937567088910","title":"Small-molecule catabolism","description":"The top GO terms cluster around catabolic metabolism of small molecules: ethanol oxidation/catabolic, retinol metabolism, GABA catabolism, putrescine catabolism, and folate-related catabolic processes. Some development terms appear but are less represented; overall the cluster seems to reflect enzymes and proteins involved in breaking down diverse small molecules rather than a single specific pathway. Therefore the label \"Small-molecule catabolism\" is representative.","confidence":"Medium","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006069","count":6},{"id":"GO:0006068","count":6},{"id":"GO:0042572","count":6},{"id":"GO:0009450","count":4},{"id":"GO:0009447","count":4}]},{"hash":"1901073622417314984","title":"Ubiquitination and protein quality control","description":"The cluster centers on ubiquitin-related processes (K63-linked ubiquitination, autoubiquitination, ERAD-related terms) and chaperone-assisted protein complex assembly, suggesting a module of ubiquitin-regulated protein quality control. Other stress-related terms (ethanol response, chitin response, glucocorticoid metabolism) point to broader regulatory roles rather than a single pathway. Confidence: Medium","confidence":"","size":6,"edges":11,"triangles":8,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0090035","count":4},{"id":"GO:0070534","count":4},{"id":"GO:0051865","count":4},{"id":"GO:0071361","count":4},{"id":"GO:0030579","count":4}]},{"hash":"2184584378608123466","title":"Fungal sterol and sphingolipid biosynthesis","description":"This cluster is dominated by fungal lipid metabolism terms, notably ergosterol biosynthetic process and mannosyl-inositol phosphorylceramide metabolic process, with supporting signals in unsaturated fatty acid biosynthesis and regulation of ergosterol biosynthesis. While some unrelated terms appear (e.g., nitrate assimilation, myelin maintenance), the strongest pattern points to fungal sterol and sphingolipid biosynthesis as the core function of these proteins.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":3},{"id":"GO:0001949","count":2},{"id":"GO:0006675","count":2},{"id":"GO:0032443","count":2},{"id":"GO:0006636","count":2}]},{"hash":"570201972316285835","title":"Amino Acid and Fatty Acid Metabolism","description":"These proteins cluster around metabolic functions: several GO terms denote biosynthesis and catabolism of amino acids (histidine, aspartate, alanine, glutamate, lysine via older term) and biotin, as well as fatty acid transport and homeostasis. A metabolic response to insulin stimulus also appears, linking energy metabolism and signaling. Taken together, the cluster represents an amino acid and fatty acid metabolic module rather than a single specific pathway.","confidence":"Medium","size":6,"edges":10,"triangles":7,"max_degree":4,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0000105","count":5},{"id":"GO:0034276","count":4},{"id":"GO:0032869","count":4},{"id":"GO:0009102","count":4},{"id":"GO:0015908","count":4}]},{"hash":"1503270407935820539","title":"Neural development and cell-cycle regulation","description":"The top GO terms point to neural development and regeneration (neurogenesis, axon extension regulation, synapse assembly, apoptosis) alongside cell-division and mitotic processes (mitotic spindle orientation, APC-dependent catabolic process) and intracellular trafficking. This suggests a cluster of proteins involved in neural differentiation and circuitry formation that also intersect with general cell-cycle and transport mechanisms, indicating a cohesive but broad theme.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0022008","count":3},{"id":"GO:0006915","count":3},{"id":"GO:0048692","count":3},{"id":"GO:0000132","count":2},{"id":"GO:0006888","count":2}]},{"hash":"764200900809954319","title":"Unknown","description":"These terms span RNA modification (tRNA/rRNA pseudouridine synthesis), DNA repair, various membrane transport processes (xenobiotic export, teichoic acid and bacteriocin transport), peroxisomal fatty acid import, and mitochondrial peptide export, with no clear shared function or interactions linking the proteins. There isn\u2019t a cohesive theme to unite the cluster, so a single functional label isn\u2019t supported.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0031119","count":1},{"id":"GO:0000455","count":1},{"id":"GO:0046618","count":1},{"id":"GO:0006289","count":1}]},{"hash":"1748265499176614204","title":"Energy metabolism and oxidative stress response","description":"This cluster centers on core energy-generating and redox-related processes: respiratory electron transport, aerobic respiration, and the TCA cycle, with supporting terms for fermentation and protein lipoylation that feed oxidoreductase complexes. Additional terms for protein modification/repair and oxidative stress response reinforce a theme of maintaining energy production and redox balance. A single outlier term on bacterial motility is noted but does not override the dominant metabolic theme.","confidence":"Medium","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0022904","count":2},{"id":"GO:0009249","count":2},{"id":"GO:0006464","count":1},{"id":"GO:0030091","count":1}]},{"hash":"387710581875720356","title":"Ubiquitin-dependent NF-\u03baB regulation","description":"This cluster is enriched for ubiquitination (GO:0016567), regulation of I-kappaB phosphorylation and NF-\u03baB\u2013related processes, and macrophage inflammatory responses, indicating proteins involved in ubiquitin-mediated control of the NF-\u03baB pathway and inflammatory signaling; a few terms about cardiac cell communication or adipocyte differentiation likely reflect incidental annotations rather than core function.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":3},{"id":"GO:0086070","count":2},{"id":"GO:1903444","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0007253","count":2}]},{"hash":"2057561380410889045","title":"Neuronal differentiation and microtubule organization","description":"The top terms point to microtubule-focused processes (cytoplasmic microtubule organization, microtubule nucleation, spindle-related assembly) as well as neural development aspects (neuron differentiation and neuron migration). This suggests a theme where neural development and neurite outgrowth are coordinated by microtubule dynamics, with some supporting signaling contexts (mechanosensory response). Confidence: Medium","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031122","count":1},{"id":"GO:0030182","count":1},{"id":"GO:1903087","count":1},{"id":"GO:0071353","count":1},{"id":"GO:1905792","count":1}]},{"hash":"872187149328384874","title":"Genome maintenance and developmental processes","description":"The GO terms show a cluster anchored in genome integrity, with multiple DNA repair-related terms (nucleotide-excision repair and UV-damage excision repair, single-strand break repair). There are also development-related terms (left/right pattern formation, endocrine system development, multicellular organism growth, EMT in endocardial cushion formation), plus transcription regulation and ribosome export signals that can accompany regulatory roles. This combination suggests proteins that participate in both genome maintenance and developmental regulation, rather than a single narrow function, justifying a label around genome maintenance intertwined with development.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":2},{"id":"GO:0060972","count":1},{"id":"GO:0000055","count":1},{"id":"GO:0035270","count":1},{"id":"GO:0000715","count":1}]},{"hash":"335055856882970387","title":"Aminoacyl-tRNA Synthetases in Translation","description":"The terms are dominated by multiple aminoacyl-tRNA synthetases (cysteinyl-, methionyl-, leucyl-, isoleucyl-, valyl-) involved in charging tRNAs for protein synthesis, along with translation and regulation of translational fidelity. This suggests a cohesive cluster centered on translation machinery and tRNA charging, with a few ancillary metabolic terms present. ","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006423","count":2},{"id":"GO:0006431","count":2},{"id":"GO:0010125","count":2},{"id":"GO:0006429","count":2},{"id":"GO:0006099","count":2}]},{"hash":"1355706809933513648","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":14,"triangles":16,"max_degree":5,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1990417","count":4},{"id":"GO:0071035","count":4},{"id":"GO:0014070","count":4},{"id":"GO:1903608","count":4},{"id":"GO:0071051","count":4}]},{"hash":"1580537292912499431","title":"Lipid and steroid metabolism","description":"The top GO terms point to lipid-based and steroid hormone\u2013related processes, including bile acid biosynthesis, fatty acid omega-oxidation, and metabolism of androgens and progesterone, as well as vitamin D\u2013related responses. While there are a few development-associated terms present (e.g., gonad development), the dominant signal centers on lipid and steroid metabolism, suggesting the cluster centers on lipid/p hormone metabolic functions rather than a single precise pathway. Confidence is Medium.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033280","count":2},{"id":"GO:0048565","count":1},{"id":"GO:0042369","count":1},{"id":"GO:0006699","count":1},{"id":"GO:0008209","count":1}]},{"hash":"1686637896287631788","title":"Ubiquitination and Proteostasis Regulation","description":"The top terms cluster around ubiquitin signaling (K63-linked ubiquitination, autoubiquitination) and protein quality control pathways (ERAD, chaperone-mediated assembly), pointing to a coherent theme of regulating protein fate via ubiquitination and proteostasis. Some stress-related terms appear, but they do not override the central ubiquitin/proteostasis pattern.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090035","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0071361","count":3},{"id":"GO:0030579","count":3}]},{"hash":"2086980331611475671","title":"Unknown","description":"The terms are highly diverse and many are obsolete, with no shared biological theme linking microtubule anchoring, development in brain/retina, dsRNA response, GPCR signaling, leptin signaling, and cell division. There are no edges connecting proteins, making it impossible to assign a cohesive, representative function to this cluster.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034454","count":1},{"id":"GO:0021756","count":1},{"id":"GO:0061087","count":1},{"id":"GO:0071360","count":1},{"id":"GO:0008277","count":1}]},{"hash":"818953051158329554","title":"Innate Immune Signaling and Antiviral Response","description":"The cluster\u2019s top GO terms converge on innate immune response, dsRNA sensing, interferon-beta production, xenophagy, and LPS/NOD2 signaling, indicating a theme of pathogen recognition and antiviral signaling. A few outliers (fat cell differentiation, telomere capping) are present but do not override the dominant immune-related functions.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045359","count":2},{"id":"GO:0046827","count":2},{"id":"GO:1904417","count":2},{"id":"GO:0032088","count":2},{"id":"GO:0031663","count":2}]},{"hash":"151257947225765231","title":"Stress-Responsive Transcriptional and Translational Regulation","description":"The top GO terms cluster around repression of RNA Pol II transcription and chromatin remodeling, with concurrent regulation of cytoplasmic translation and stress-responsive signaling (e.g., GCN2) that modulates translation during stress conditions such as UV exposure and nutrient starvation. This points to a cohesive set of proteins coordinating transcriptional and translational control under stress.","confidence":"Medium","size":6,"edges":10,"triangles":7,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0000122","count":3},{"id":"GO:0043044","count":2},{"id":"GO:0042766","count":2},{"id":"GO:0031953","count":1},{"id":"GO:1904803","count":1}]},{"hash":"1803586988025273853","title":"Diverse solute transporters","description":"This cluster centers on transmembrane transport of a variety of solutes (nitrate, nitrite, arabinose, glucose, urate, trehalose, dehydroascorbic acid, sodium ions), indicating membrane transporter proteins with different substrates rather than a single specific pathway. The diverse transport terms dominate over the single replicative senescence term, supporting a broad transporter theme.","confidence":"High","size":6,"edges":8,"triangles":0,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":3},{"id":"GO:1904728","count":2},{"id":"GO:0015751","count":2},{"id":"GO:0044381","count":2},{"id":"GO:0015747","count":2}]},{"hash":"1329368436022786725","title":"Spliceosome-Driven mRNA Processing Complex","description":"The top GO terms are centered on mRNA splicing via the spliceosome, regulation of alternative splicing, splice-site recognition, and components involved in small-subunit processome assembly, all pointing to core RNA processing and splicing machinery. Additional terms related to mRNA modification and ncRNA- and miRNA-mediated gene silencing suggest broader RNA processing/regulation connections, while a development term (blastocyst formation) is less directly informative for the cluster\u2019s primary function. Overall, the cluster appears to represent proteins involved in RNA splicing and mRNA maturation, with linked RNA-regulation activities.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0000381","count":2},{"id":"GO:0016556","count":2},{"id":"GO:0001825","count":2}]},{"hash":"917851824812954635","title":"Cell cycle regulation and transcription control","description":"The top GO terms point to processes governing cell cycle progression and division (mitotic cell cycle, cell division, meiosis I, cell population proliferation) together with transcriptional regulation (regulation of transcription by RNA polymerase II, positive regulation of DNA-templated transcription) and CDK activity regulation. This suggests a cluster of proteins that coordinate cell proliferation with transcriptional programs, possibly including CDK regulators and transcriptional regulators. Some terms reference developmental or historical annotations (histoblast morphogenesis, nucleosome density) but do not change the overall theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007346","count":1},{"id":"GO:0007049","count":1},{"id":"GO:0051301","count":1},{"id":"GO:0045737","count":1},{"id":"GO:0060303","count":1}]},{"hash":"296209649635441844","title":"Unknown","description":"The top GO terms are a scattered mix spanning redox balance, TOR signaling, transcription control, protein localization, and wing morphogenesis, with several terms marked obsolete. There is no single, cohesive biological process tying all six proteins together, so a reliable, specific label cannot be assigned. ","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902376","count":1},{"id":"GO:0045454","count":1},{"id":"GO:0036129","count":1},{"id":"GO:1903361","count":1},{"id":"GO:0031929","count":1}]},{"hash":"754580508539262633","title":"Multilineage differentiation","description":"The top GO terms span differentiation and morphogenesis across multiple tissues and lineages (e.g., lamellocyte, R7 photoreceptor, neuromast hair cells, forebrain, endocardial differentiation, and boundary formation), indicating a broad developmental theme rather than a single pathway. This suggests the cluster groups proteins involved in diverse lineage specification and tissue morphogenesis.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060288","count":1},{"id":"GO:0060665","count":1},{"id":"GO:1904937","count":1},{"id":"GO:0046716","count":1},{"id":"GO:0048903","count":1}]},{"hash":"1824951592412322185","title":"Proteostasis under Heat Stress","description":"This cluster is best labeled Proteostasis under Heat Stress because the terms cluster around protein folding in the endoplasmic reticulum, unfolded protein response, heat-related stress responses, and ubiquitin-proteasome\u2013mediated quality control, all core aspects of cellular proteostasis under stress. Some terms like DNA replication and translational frameshifting are less directly linked and may represent broader cellular processes included in the group, but the dominant theme is protein homeostasis under heat stress.","confidence":"Medium","size":6,"edges":10,"triangles":7,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":6},{"id":"GO:0006260","count":6},{"id":"GO:1900035","count":6},{"id":"GO:1901621","count":6},{"id":"GO:0034975","count":6}]},{"hash":"50849619743089898","title":"Neuronal development and synaptic regulation","description":"The terms cluster around neural development and function: regulation of dendritic spine morphogenesis, interneuron migration, and cell polarity maintenance point to neural development; GPCR acetylcholine signaling and regulation of the secretory pathway suggest neuronal signaling and trafficking; mitochondrion-ER tethering may support neuron-specific energy and calcium handling. The mix indicates a broader neural development/synaptic regulation theme rather than a single precise function, hence this label.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0061001","count":1},{"id":"GO:1990456","count":1},{"id":"GO:1902542","count":1},{"id":"GO:0034332","count":1},{"id":"GO:0007213","count":1}]},{"hash":"922665524130166715","title":"Spliceosome-mediated RNA processing and transcription control","description":"The top GO terms cluster around splicing (alternative and cis splicing via the spliceosome) and transcriptional regulation by RNA polymerase II, indicating the proteins are mainly involved in RNA processing and control of transcription rather than other developmental morphogenesis processes. ","confidence":"Medium","size":6,"edges":12,"triangles":11,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":3},{"id":"GO:0045292","count":2},{"id":"GO:0006378","count":2},{"id":"GO:0071600","count":2},{"id":"GO:0045023","count":2}]},{"hash":"821067030963725891","title":"Transcriptional Regulation & Chromatin Remodeling","description":"The top GO terms point to transcriptional control (DNA-templated transcription and negative regulation of transcription by RNA Pol II) and chromatin remodeling, suggesting these proteins function as a transcriptional regulation module. Several terms also hint at differentiation-related processes (megakaryocyte/erythrocyte differentiation) and stem cell proliferation, indicating a role in lineage commitment rather than metabolism. Some obsolete terms are present but do not alter the overall theme.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043046","count":4},{"id":"GO:0045654","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0043044","count":2}]},{"hash":"1562482113563282313","title":"Unknown","description":"The top GO terms are highly diverse and span oxidative stress response, muscle and heart development, reproductive implantation, endocrine signaling, neuronal activity, and even an obsolete histone isomerization term. With no single shared pathway or process tying these terms together, and only a few proteins, there isn\u2019t a coherent function to label; thus Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042542","count":2},{"id":"GO:0046716","count":2},{"id":"GO:0007566","count":2},{"id":"GO:0030073","count":1},{"id":"GO:0032925","count":1}]},{"hash":"980525353731861394","title":"Ubiquitin-Dependent Nuclear RNA Export and Transcription Regulation","description":"The terms show a clear thread around ubiquitin-related processes (autoubiquitination, ubiquitin-dependent catabolic processes) and regulators of transcription and RNA export (mRNA and tRNA export from the nucleus). Although other GO terms (Wnt signaling, ribophagy, synapse-related processes) appear, the strongest cohesive signal is ubiquitin-mediated control affecting nuclear RNA handling and transcription, suggesting this cluster centers on ubiquitin-linked regulation of nuclear RNA export and transcription.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0045944","count":3},{"id":"GO:0042787","count":3},{"id":"GO:0034517","count":2}]},{"hash":"1808580062712432136","title":"Transmembrane Ion and Water Transport","description":"This cluster centers on proteins involved in transporting ions across membranes (nitrate, chloride, protons, potassium, monoatomic anions, iron) and in transepithelial water movement, along with related pH response and cell volume regulation. The collective GO terms point to a shared function in maintaining ionic and osmotic balance across membranes, with a possible incidental tissue-specific development term. Therefore, a concise label focusing on membrane ion and water transport best captures the common theme.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045794","count":1},{"id":"GO:0015706","count":1},{"id":"GO:1902476","count":1},{"id":"GO:0010447","count":1},{"id":"GO:0035377","count":1}]},{"hash":"141442366194509685","title":"Transcription Regulation and RNA Processing","description":"This cluster centers on gene expression control, with terms for regulating DNA-templated transcription, pre-miRNA processing, miRNA turnover, transcription antitermination, and mRNA stabilization. A chromatin-related hint (historical histone exchange) reinforces a broader regulatory theme at both transcriptional and post-transcriptional levels.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043486","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0035019","count":1},{"id":"GO:1902219","count":1},{"id":"GO:0010587","count":1}]},{"hash":"1089501177056993859","title":"Plant Cell Wall Biosynthesis and Glycosylation","description":"Most terms point to plant cell wall polysaccharide biosynthesis (mucilage, homogalacturonan, glucuronoxylan, plant-type secondary cell wall biogenesis) and related sugar metabolism/glycosylation, suggesting a cell wall-focused cluster. An outlier term about skeletal muscle tissue regeneration is present but does not fit the plant cell wall theme.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010192","count":1},{"id":"GO:0010289","count":1},{"id":"GO:0010417","count":1},{"id":"GO:0043403","count":1},{"id":"GO:0071555","count":1}]},{"hash":"2121292271119524237","title":"Virus-host lifecycle proteins","description":"The top GO terms are dominated by viral lifecycle processes: virion assembly, viral release, integrated proviral latency, and host-mediated activation of viral genome replication, with additional host entry/symbiont terms. This coherence supports naming the cluster after virus\u2013host interactions and viral lifecycle, despite a couple unrelated terms likely due to annotation noise.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1901407","count":3},{"id":"GO:0051301","count":2},{"id":"GO:2000276","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0048453","count":2}]},{"hash":"1938429785330431684","title":"Plant nuclear transcription and chromatin remodeling","description":"This cluster is dominated by terms for chromatin remodeling and DNA-templated transcription (chromatin remodeling, DNA-templated transcription, snRNA transcription), with plant-specific processes such as gibberellin response and trichome patterning suggesting a plant nuclear regulatory role. The absence of edges implies these proteins may be functionally related but not tightly connected in the current network, yet the core theme remains chromatin-based transcription regulation in plants.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043044","count":2},{"id":"GO:0042391","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0071320","count":2},{"id":"GO:0009739","count":1}]},{"hash":"531119249069788350","title":"ER Stress and Protein Folding","description":"The cluster is dominated by endoplasmic reticulum\u2013associated quality-control terms: protein folding in the ER and response to unfolded protein, which together point to ER stress and the unfolded protein response. Additional terms related to translation and heat response support a broader cellular stress/quality-control theme, though a few items (like DNA replication and developmental signaling) appear less connected and may be background noise.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":1},{"id":"GO:0009408","count":1},{"id":"GO:0006260","count":1},{"id":"GO:1900035","count":1},{"id":"GO:1901621","count":1}]},{"hash":"402154153344983731","title":"Virus-host interaction and viral life cycle","description":"Most of the top GO terms center on viral processes: virion assembly, viral life cycle, viral release, proviral latency, and host-mediated activation of viral genome replication, which together point to virus\u2013host interactions and the viral life cycle. A few terms (sepal formation, protein folding, leukocyte migration) are more general or incidental, but they do not outweigh the viral-centric theme. Thus, the cluster is best described as virus-host interaction and replication.","confidence":"Medium","size":6,"edges":5,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:2000276","count":2},{"id":"GO:0019068","count":2},{"id":"GO:0048453","count":2},{"id":"GO:0075713","count":2},{"id":"GO:0006457","count":2}]},{"hash":"1126379843741866243","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0046380","count":1},{"id":"GO:0046839","count":1},{"id":"GO:0032361","count":1},{"id":"GO:0046050","count":1},{"id":"GO:0097755","count":1}]},{"hash":"1400916050555969350","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000462","count":2},{"id":"GO:0000480","count":1},{"id":"GO:0000447","count":1},{"id":"GO:0009561","count":1},{"id":"GO:0000472","count":1}]},{"hash":"1739427641848129379","title":"Ribosome Biogenesis & rRNA Maturation","description":"This cluster is dominated by GO terms tied to ribosome construction and rRNA processing/maturation (including maturation of SSU and LSU rRNA, nucleolus organization, and rRNA processing regulation), indicating a cohesive role in ribosome assembly and maturation.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0000463","count":1},{"id":"GO:0044786","count":1},{"id":"GO:2000232","count":1},{"id":"GO:0042273","count":1}]},{"hash":"1911735438525287334","title":"Translation initiation and ribosome assembly","description":"This cluster centers on translation-related processes: multiple GO terms point to translation, cytoplasmic/ translational initiation, formation of the translation preinitiation complex, cytosolic ribosome assembly, and eIF4F complex assembly, indicating involvement in the translation initiation machinery. A couple of less connected terms (oligodendrocyte development, male germ cell proliferation) appear but are represented by single instances and do not define the cluster\u2019s core function. Overall, the dominant theme is the assembly and initiation of the protein synthesis machinery.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1905618","count":1},{"id":"GO:0014003","count":1},{"id":"GO:0045947","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0006413","count":1}]},{"hash":"848825895257233895","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":4},{"id":"GO:0048701","count":4},{"id":"GO:1990417","count":3},{"id":"GO:0071035","count":3},{"id":"GO:0014070","count":3}]},{"hash":"1808816964979735671","title":"Unknown","description":"The top GO terms span immune defense, cellular stress responses, metabolism, and neural development, with no single coherent theme tying all functions together, so a unified label is not supported.","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0050830","count":6},{"id":"GO:0071333","count":6},{"id":"GO:0016477","count":5},{"id":"GO:0010898","count":5},{"id":"GO:0022038","count":5}]},{"hash":"818950429861226787","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0008615","count":1},{"id":"GO:0006982","count":1},{"id":"GO:0009229","count":1}]},{"hash":"385202398326401149","title":"Unknown","description":"The top GO terms span a mix of bacterial stress responses (SOS response, response to antibiotic, bacteriocin transport/immunity, teichoic acid transport) and unrelated eukaryotic processes (nucleotide-excision repair, long-chain fatty acid import into peroxisomes, oligopeptide export from mitochondrion), with no single coherent function uniting the cluster. Although DNA damage response appears in a couple of terms, the overall set lacks a clear shared theme across all proteins, making a specific, confident label inappropriate.","confidence":"","size":6,"edges":6,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009432","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0045944","count":2},{"id":"GO:0046618","count":1},{"id":"GO:0006289","count":1}]},{"hash":"696058368223408425","title":"Sulfur amino acid metabolism and H2S biosynthesis","description":"Top GO terms cluster around sulfur-containing amino acid metabolism (serine/cysteine/homocysteine), transsulfuration, and hydrogen sulfide production, with links to related pyruvate flux and detoxification (cyanide). This points to a cohesive set of enzymes handling sulfur amino acids and sulfide, justifying the label.","confidence":"High","size":6,"edges":15,"triangles":20,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0006565","count":4},{"id":"GO:0019343","count":3},{"id":"GO:0019346","count":3},{"id":"GO:0070814","count":3},{"id":"GO:0043278","count":2}]},{"hash":"1087363466317291641","title":"Unknown","description":"The top terms span diverse metabolic biosynthesis processes (pyruvate, isoleucine, 2-oxobutyrate, coenzyme M, cyanide, homocysteine) and a few cellular response categories (apoptotic process, translation regulation), with no single unifying function across the cluster. Several terms are obsolete, and only a few proteins link to each term, making a coherent, specific label unlikely. ","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009097","count":2},{"id":"GO:0006915","count":2},{"id":"GO:2000767","count":2},{"id":"GO:0043278","count":1},{"id":"GO:0042866","count":1}]},{"hash":"448071758306661512","title":"Secretory pathway folding and trafficking","description":"This cluster is dominated by terms for protein folding, unfolding, chaperone-dependent refolding, ER unfolded protein response, and vesicle transport between ER and Golgi and within the Golgi, as well as mitochondrial import. While DNA replication-related terms appear, they are less aligned with the main theme, suggesting some overlap but a stronger link to protein maturation and trafficking overall. Medium","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":6},{"id":"GO:0034214","count":4},{"id":"GO:0033314","count":4},{"id":"GO:0006888","count":4},{"id":"GO:0070389","count":4}]},{"hash":"315167658177916685","title":"Unknown","description":"There are no GO terms or connections to define a shared function, so a meaningful label cannot be derived from this cluster.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"62366314640081923","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0035606","count":1},{"id":"GO:0051402","count":1},{"id":"GO:0009089","count":1},{"id":"GO:0008615","count":1},{"id":"GO:0055114","count":1}]},{"hash":"871973208641156174","title":"Lipid and pigment biosynthesis","description":"This cluster\u2019s top GO terms center on biosynthetic processes for lipids and pigments, including fatty acid elongation, mycolic acid biosynthesis, poly-hydroxybutyrate biosynthesis, and steroid biosynthesis (androgen and glucocorticoid). The presence of melanin biosynthesis further supports a pigment-related theme. While there are a couple of broader terms (lung development, transcription regulation), the dominant pattern is lipid- and pigment-producing pathways, suggesting a cohesive functional theme for these proteins. ","confidence":"Medium","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0008209","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0006710","count":1},{"id":"GO:0030324","count":1},{"id":"GO:0045150","count":1}]},{"hash":"2215337853664658753","title":"Unknown","description":"The GO terms are highly diverse, covering bacterial biosynthetic processes (poly-hydroxybutyrate, mycolic acid, acetoin) and unrelated vertebrate processes (lung development, androgen/glucocorticoid metabolism) plus transcription regulation, with no shared pathway or functional theme and no network connectivity observed, so there is no clear, cohesive cluster function to name.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042619","count":3},{"id":"GO:0055114","count":3},{"id":"GO:0008209","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006710","count":2}]},{"hash":"1271172821698004430","title":"LPS and O-antigen biosynthesis","description":"This cluster is dominated by GO terms related to lipopolysaccharide biosynthesis, including LPS biosynthetic process, core region biosynthesis, and O antigen biosynthesis, plus dTDP-rhamnose biosynthesis, suggesting a shared role in LPS assembly and sugar moiety production. A transcription-related term and a few other unrelated terms may reflect annotation noise or multifunctionality, but the core enrichment points to the LPS biosynthesis pathway.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045226","count":2},{"id":"GO:0009244","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0009103","count":2},{"id":"GO:0019305","count":2}]},{"hash":"611959915982917626","title":"Unknown","description":"The top GO terms cover a very broad and seemingly unrelated mix of processes (oxidation-reduction, antibiotic biosynthesis, androgen metabolism and catabolism, transcription regulation, lung development, steroid biosynthesis, melanin and mycolic acid biosynthesis). There is no single coherent biological theme tying these proteins together, and the presence of an obsolete term further suggests inconsistency. Because of this lack of a clear, shared function, a specific, representative label is not justifiable.","confidence":"","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0055114","count":5},{"id":"GO:0017000","count":5},{"id":"GO:0008209","count":4},{"id":"GO:0006355","count":4},{"id":"GO:0006710","count":4}]},{"hash":"236938673941867215","title":"Mitochondrial respiration and electron transport","description":"The GO terms show a strong emphasis on aerobic respiration, the TCA cycle, mitochondrial electron transport (succinate to ubiquinone), and cytochrome complex assembly, pointing to proteins involved in mitochondrial energy production. Although there are a few light-/photosynthesis-related terms, the core signal is mitochondrial energy metabolism.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009060","count":1},{"id":"GO:0006099","count":1},{"id":"GO:0006121","count":1},{"id":"GO:0017004","count":1},{"id":"GO:0071486","count":1}]},{"hash":"1584663777907253727","title":"Unknown","description":"The top GO terms are highly diverse (bioluminescence, GTPase regulation, nuclear import, dephosphorylation, various catabolic and biosynthetic metabolism, seed coat development), with no clear unified function tying the proteins together, and the cluster has no edges or interactions, suggesting it does not reflect a single cohesive biological role.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008218","count":2},{"id":"GO:0043547","count":2},{"id":"GO:0006607","count":2},{"id":"GO:0006470","count":2},{"id":"GO:0010124","count":1}]},{"hash":"1622892494009760108","title":"Diverse Metabolite Biosynthesis","description":"This cluster is dominated by GO terms describing biosynthetic processes for a variety of small molecules and pigments (retinol/retinal, glucocorticoids, androgens, melanin, tropane alkaloids, antibiotics) and a polymer biosynthesis term (PHB). Although there is some diversity and a few outliers (e.g., a developmental term), the common theme is the synthesis of diverse metabolites, which justifies this label. ","confidence":"Medium","size":6,"edges":4,"triangles":0,"max_degree":4,"top_function":"respiratory system process","top_go_terms":[{"id":"GO:0042572","count":4},{"id":"GO:0017000","count":4},{"id":"GO:0008209","count":3},{"id":"GO:0030324","count":3},{"id":"GO:0045150","count":3}]},{"hash":"1980007030645087330","title":"Unknown","description":"The GO terms span development, cell differentiation, cell cycle, metabolism, RNA modification, and cofactor biosynthesis with no single shared function across the six proteins, indicating a heterogeneous annotation rather than a cohesive cluster.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0021510","count":1},{"id":"GO:0035335","count":1},{"id":"GO:0002143","count":1},{"id":"GO:0018192","count":1},{"id":"GO:0030855","count":1}]},{"hash":"979599197352844519","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0009236","count":2},{"id":"GO:0001081","count":1},{"id":"GO:0009718","count":1}]},{"hash":"1613309343995465694","title":"Regulators of cellular signaling and survival","description":"The GO terms point to regulatory roles across diverse processes\u2014cell cycle control, toll-like receptor signaling, transcriptional repression, apoptosis and necroptosis regulation, ubiquitination, and protein stabilization\u2014along with regulatory aspects of organelle interactions, granule maturation, and synapse organization. This pattern suggests proteins that modulate signaling and cell fate rather than acting as core structural components, justifying a label focused on regulatory roles in signaling and survival.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":1},{"id":"GO:0034121","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0000209","count":1}]},{"hash":"593017415405304987","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006364","count":2},{"id":"GO:0090503","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0006369","count":2}]},{"hash":"1794407324651710414","title":"ER Protein Folding and Heat Stress Response","description":"The cluster is enriched for GO terms related to protein folding in the endoplasmic reticulum, responses to heat and unfolded proteins, and ER-associated quality control, suggesting these proteins act as ER chaperones or regulators of the unfolded protein response under heat stress. Other terms like translational frameshifting or DNA replication may reflect broader stress-related regulation but are less central to the main theme.","confidence":"High","size":6,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006469","count":4},{"id":"GO:0009408","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1900035","count":3},{"id":"GO:1901621","count":3}]},{"hash":"166014132493818190","title":"Mitochondrial Transport and Energy Regulation","description":"The proteins show a clear focus on mitochondria, with transport of ADP, ATP, alpha-ketoglutarate, and magnesium ions, plus regulation of mitochondrial membrane permeability and membrane potential. The inclusion of insulin/IGF signaling responses and oxidative stress further ties these proteins to mitochondrial energy management and metabolic signaling.","confidence":"High","size":6,"edges":2,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":2},{"id":"GO:0051881","count":2},{"id":"GO:0015742","count":2},{"id":"GO:0032869","count":2},{"id":"GO:1990314","count":2}]},{"hash":"1163840455615201572","title":"ER stress response and redox homeostasis","description":"Most of the top terms center on endoplasmic reticulum (ER) stress response (GO:0034976), cellular oxidant detoxification (GO:0098869), and redox homeostasis (GO:0045454), plus ER-Golgi and Golgi-to-plasma membrane transport terms. This suggests a cluster of proteins involved in maintaining ER function and oxidative balance, with some associated trafficking between ER and Golgi. Minor terms like strigolactone response and xenobiotic degradation are present but less central.","confidence":"Medium","size":6,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0034976","count":2},{"id":"GO:1903206","count":2},{"id":"GO:0045454","count":2}]},{"hash":"1795951141151705332","title":"Mitochondrial Transport and Metabolic Regulation","description":"Dominant terms describe mitochondrial transport and energetics (regulation of membrane permeability and membrane potential, mitochondrial ATP transmembrane transport, alpha-ketoglutarate transport) along with metabolic signaling (cellular response to insulin/IGF). This points to a cluster centered on mitochondrial transport tied to energy metabolism, with a few peripheral processes. ","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006836","count":1},{"id":"GO:0051260","count":1},{"id":"GO:2000372","count":1},{"id":"GO:0016567","count":1},{"id":"GO:0046902","count":1}]},{"hash":"1329760158662676831","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006458","count":2},{"id":"GO:0030073","count":1},{"id":"GO:0032925","count":1},{"id":"GO:1901710","count":1},{"id":"GO:0055010","count":1}]},{"hash":"1342824990502397601","title":"Stem cell proliferation and multilineage differentiation","description":"The terms point to growth and differentiation across multiple lineages: stem cell proliferation, erythrocyte differentiation (including primitive erythrocyte differentiation), and neuron maturation, along with general cell population proliferation. Supporting metabolism terms (thiamine/folate pathways) and hormone biosynthesis fit with cellular development and differentiation. This suggests a broad developmental/proliferative theme rather than a single, specific pathway.","confidence":"Medium","size":6,"edges":8,"triangles":5,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0046886","count":2},{"id":"GO:0045648","count":2},{"id":"GO:0009228","count":2},{"id":"GO:0046653","count":2},{"id":"GO:2000648","count":2}]},{"hash":"1806813489638309616","title":"Photosynthesis Light Response","description":"Top GO terms center on photosynthesis and light-response processes, including photosynthesis, light harvesting in photosystem II, nonphotochemical quenching, and responses to red, blue, and UV-A light as well as light intensity changes. This pattern suggests chloroplast-associated photobiology and light-driven energy capture, justifying a label around photosynthesis and light response.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071486","count":1},{"id":"GO:0009645","count":1},{"id":"GO:0018298","count":1},{"id":"GO:1904964","count":1},{"id":"GO:0010114","count":1}]},{"hash":"1279934541418607107","title":"Unknown","description":"The top terms show plant secondary metabolite biosynthesis (flavonol, melatonin) and lignin formation, but also nucleic acid\u2013related and viral integration processes, which do not form a single coherent functional theme. This mixed signal makes a precise, representative label difficult. ","confidence":"","size":6,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032259","count":2},{"id":"GO:0051555","count":2},{"id":"GO:0030187","count":2},{"id":"GO:0009809","count":2},{"id":"GO:0090502","count":2}]},{"hash":"1588224585442790546","title":"Sugar and nucleotide metabolism","description":"The proteins show a mix of sugar-related processes (glycolysis via fructose-6-phosphate, carbohydrate phosphorylation, various sugar catabolic pathways) and nucleotide salvage/biosynthesis (adenosine salvage, AMP/dATP biosynthesis), indicating a broad theme around sugar and nucleotide metabolism rather than a single specific pathway.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0061615","count":3},{"id":"GO:0009750","count":3},{"id":"GO:0097171","count":3},{"id":"GO:0006169","count":3},{"id":"GO:0006175","count":3}]},{"hash":"573044014060406847","title":"Cofactor and sulfur amino acid biosynthesis","description":"The cluster shows strong representation of sulfur-containing amino acid biosynthesis (L-cysteine, hydrogen sulfide) and cofactor biosynthesis (biotin, vitamin E), indicating a metabolic biosynthesis theme. A handful of RNA modification terms are present but less prominent, suggesting secondary roles. Overall, the main signal is biosynthesis of sulfur amino acids and cofactors.","confidence":"Medium","size":6,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0019344","count":2},{"id":"GO:0070814","count":2},{"id":"GO:0018027","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0035690","count":1}]},{"hash":"826013086588181091","title":"Diverse biosynthetic pathways","description":"GO terms point to amino acid biosynthesis (methionine, homoserine, threonine), lipid/isoprenoid biosynthesis (cholesterol, mevalonate, farnesyl diphosphate, IPP), and carbohydrate metabolism (galactose, galacturonate, GDP-L-fucose salvage). This broad mix suggests a cluster centered on diverse biosynthetic/metabolic processes rather than a single, cohesive pathway, so a general label like Diverse biosynthetic pathways is appropriate.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009086","count":3},{"id":"GO:0006695","count":2},{"id":"GO:0009092","count":2},{"id":"GO:0000435","count":2},{"id":"GO:0061623","count":2}]},{"hash":"1457706679162250656","title":"Transmembrane Solute Transporters","description":"The cluster's GO terms cluster around transmembrane transport of diverse substrates (nitrite, nitrate, phosphate ions, sugars like galactose and fucose, vitamins, sodium) and related vesicular transport. This suggests a group of membrane transport proteins with broad substrate specificity rather than a single substrate.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015707","count":3},{"id":"GO:0035435","count":3},{"id":"GO:0015706","count":3},{"id":"GO:0006004","count":3},{"id":"GO:0015757","count":3}]},{"hash":"1013357340871708306","title":"Fungal protein folding and ER stress response","description":"The top GO terms cluster around protein quality control, including unfolded protein response, chaperone-assisted refolding, and cellular responses to heat/ER stress, indicating a focus on protein folding maintenance. Some fungal-specific terms (beta-glucan biosynthesis, karyogamy) suggest a fungal context, but the core theme appears to be protein folding and stress response mechanisms.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070389","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0070880","count":1},{"id":"GO:1903382","count":1},{"id":"GO:1902037","count":1}]},{"hash":"497071007274359031","title":"Unknown","description":"The top GO terms span very disparate functions: nuclear RNA processing (transcription termination, mRNA splicing), mitotic processes (spindle assembly, chromatid cohesion), cell morphogenesis, and bacterial biosynthetic processes (lipid A and LPS biosynthesis), with several obsolete terms. This mixture suggests no single coherent functional theme for all six proteins, likely due to annotation noise or cross-species misannotations. ","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006369","count":2},{"id":"GO:0045292","count":2},{"id":"GO:1904908","count":2},{"id":"GO:0051225","count":2},{"id":"GO:0009245","count":2}]},{"hash":"1447487044013236199","title":"Unknown","description":"Unknown","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":5},{"id":"GO:0007283","count":5},{"id":"GO:0043547","count":5},{"id":"GO:0061158","count":4},{"id":"GO:0010875","count":4}]},{"hash":"1579879432775921042","title":"Unknown","description":"There are no edges or GO terms to suggest a shared function among the proteins, and the ReCIPE note does not provide a functional theme. Without a cohesive motif, a meaningful label cannot be assigned.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"388904546282081029","title":"Unknown","description":"The top GO terms are highly diverse, spanning aging, GTPase signaling, mechanosensory detection, apoptosis regulation, B cell signaling, RNA biosynthesis regulation, fatty acid response, spermatogenesis, dephosphorylation, and phototropism. There is no single coherent biological function that connects these terms for this cluster, and with no edges or coherent overlap, a concise, specific label is not warranted.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007568","count":3},{"id":"GO:0043547","count":3},{"id":"GO:1905789","count":2},{"id":"GO:0043066","count":2},{"id":"GO:0050853","count":2}]},{"hash":"2164260204288285223","title":"RNA processing and ribosome biogenesis","description":"The cluster centers on RNA maturation and translation-related processes: spliceosomal mRNA splicing, tRNA acetylation and wobble modification, rRNA maturation, and ribosomal small subunit biogenesis, suggesting a shared role in RNA processing and ribosome assembly. Some telomere/DNA regulation terms are present but appear peripheral to the main RNA-centric theme.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032211","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0006310","count":2},{"id":"GO:0048026","count":2},{"id":"GO:1904812","count":1}]},{"hash":"348465185452018422","title":"RNA processing and transcription regulation","description":"The GO terms point strongly to nuclear roles in gene expression: negative regulation of transcription by RNA polymerase II, mRNA capping, rRNA modification, and histone-related methylation all suggest transcription control and RNA processing/chromatin regulation. While biosynthetic terms appear, they are comparatively fewer and less cohesive with the main signal. Overall, the core theme is RNA processing and transcription regulation, with chromatin modifications accompanying this function.","confidence":"High","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0014075","count":3},{"id":"GO:0000122","count":2},{"id":"GO:0018027","count":2},{"id":"GO:0006370","count":2},{"id":"GO:0035690","count":2}]},{"hash":"1087991076195917180","title":"Synaptic organization and vesicle cycling","description":"The top GO terms cluster around synaptic structure and function: synapse organization, regulation of synaptic vesicle endocytosis, receptor internalization, terminal button organization, and modulation of postsynaptic potentials. A few terms (cellulose catabolic process, cholesterol biosynthetic process, osteoblast development) appear as outliers, likely reflecting broader annotations or cross-species hits, but the dominant signal points to neuronal synaptic regulation and vesicle trafficking.","confidence":"Medium","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":2},{"id":"GO:0006695","count":1},{"id":"GO:2000331","count":1},{"id":"GO:0051262","count":1},{"id":"GO:0050808","count":1}]},{"hash":"2040778502535108674","title":"Protein acetylation and amine metabolism","description":"The top GO terms cluster around acetylation events (N-terminal acetylation, peptidyl-lysine acetylation, spermine and histone acetylation) and related amine/acetyl group metabolism (putrescine, N-acetylglucosamine, acetoin). This suggests a functional group centered on protein modification by acetyl groups, with some peripheral metabolism terms. Overall, a cohesive label is \"protein acetylation and amine metabolism.\"","confidence":"High","size":6,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009447","count":3},{"id":"GO:0018003","count":3},{"id":"GO:2000025","count":3},{"id":"GO:0006044","count":3},{"id":"GO:0032919","count":3}]},{"hash":"1721142397018127294","title":"Unknown","description":"The top GO terms span transcription, kinase regulation, spermatid development, magnetoreception, glucocorticoid regulation, gravitaxis, circadian calcium oscillation, locomotor rhythm, meristem growth, and light-response\u2014covering diverse processes across different organisms with no clear common function. There are no network edges to tie these proteins into a single pathway, so there isn\u2019t a coherent, specific theme to label beyond Unknown.","confidence":"","size":6,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006351","count":2},{"id":"GO:0033674","count":1},{"id":"GO:0007286","count":1},{"id":"GO:0050958","count":1},{"id":"GO:2000850","count":1}]},{"hash":"431277472725922059","title":"Bacterial DNA replication and damage response","description":"The top terms cluster around bacterial DNA processes: rolling circle and bacterial-type DNA replication, homologous recombination repair, and the SOS response, along with defenses against foreign intracellular DNA and virus defense. Some terms are obsolete or likely unrelated (nephrocyte differentiation), but the core signal points to DNA replication and DNA damage response in bacteria.","confidence":"High","size":6,"edges":9,"triangles":5,"max_degree":5,"top_function":null,"top_go_terms":[{"id":"GO:0090305","count":2},{"id":"GO:0043388","count":2},{"id":"GO:0070581","count":1},{"id":"GO:0044787","count":1},{"id":"GO:0061321","count":1}]},{"hash":"1699197932827989958","title":"Proteasomal Ubiquitination and Cell Cycle Control","description":"This cluster is driven by ubiquitin-related processes (SCF-dependent proteolysis, polyubiquitination, K27- and K11-linked ubiquitination) and cell cycle events (chromosome segregation, mitotic checkpoints). The common theme is proteins that tag or recognize substrates for degradation to regulate the cell cycle and chromosome dynamics, with incidental signaling links (e.g., NF-kappaB modulation). ","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"chromatin organization","top_go_terms":[{"id":"GO:0051965","count":5},{"id":"GO:0031146","count":5},{"id":"GO:0051092","count":5},{"id":"GO:1902916","count":5},{"id":"GO:0009737","count":5}]},{"hash":"1594175855289353621","title":"Unknown","description":"These terms cover a wide range of cellular processes with little overlap: negative regulation of mitochondrial fusion, ERAD maintenance, heat acclimation, store-operated calcium channel regulation, spindle pole body duplication, erythrocyte differentiation, protein autoubiquitination, ribosomal small subunit assembly, and nucleotide-excision repair. There isn\u2019t a single cohesive theme or pathway tying them together, suggesting diverse or multi-functional roles or annotation noise. Therefore, a single intuitive label cannot be justified.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010637","count":5},{"id":"GO:1904378","count":5},{"id":"GO:0010286","count":5},{"id":"GO:1901340","count":5},{"id":"GO:0014070","count":5}]},{"hash":"48587017657553918","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":9,"triangles":7,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0071441","count":5},{"id":"GO:0001178","count":5},{"id":"GO:1990417","count":5},{"id":"GO:0071035","count":5},{"id":"GO:0014070","count":5}]},{"hash":"1050536990362223508","title":"Unknown","description":"The top GO terms are highly heterogeneous, covering cholesterol biosynthesis, aromatic compound and nitrate catabolism, development of gonads and retinal vasculature, and various signaling and cell adhesion processes. There is no clear, single function tying these proteins together, so a specific label cannot be confidently assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":1},{"id":"GO:0046232","count":1},{"id":"GO:0008585","count":1},{"id":"GO:1901206","count":1},{"id":"GO:0031284","count":1}]},{"hash":"1716869891032698093","title":"Androgen signaling in male reproductive development","description":"This cluster\u2019s most represented terms are male sex differentiation and prostate gland development, along with steroid hormone receptor complex assembly, which together point to androgen signaling in male reproductive biology. The remaining terms (cell division, interferon response, metabolism, ion transport, and vascular regulation) are less dominant and may reflect broader or incidental annotations. Overall, the proteins are best described as related to androgen-mediated development rather than a single, cohesive other function.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046661","count":2},{"id":"GO:0030850","count":2},{"id":"GO:0006463","count":2},{"id":"GO:0051301","count":2},{"id":"GO:0071357","count":1}]},{"hash":"655048467598118743","title":"Unknown","description":"The top terms cover a mix of mitochondrial dynamics, ER-associated stress, heat response, calcium signaling, cell cycle-related spindle pole body duplication, differentiation, ubiquitination, ribosome assembly, and DNA repair, with no single cohesive function emerging to unify the cluster. Therefore, I cannot assign a concise, representative label. ","confidence":"","size":5,"edges":7,"triangles":4,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0010637","count":5},{"id":"GO:1904378","count":5},{"id":"GO:0010286","count":5},{"id":"GO:1901340","count":5},{"id":"GO:0014070","count":5}]},{"hash":"1367145645789980892","title":"Mitochondrial tRNA aminoacylation and translation","description":"These proteins cluster around mitochondrial tRNA charging for multiple amino acids (serine, glycine, threonine, histidine, proline) and associated translation-related processes, indicating a shared role in mitochondrial protein synthesis. The presence of terms for L-selenocysteine incorporation and regulation of translational fidelity reinforces a translation-focused function within mitochondria, while a couple of broader terms (DNA biosynthesis, embryonic development) are less directly connected. Overall, the dominant signal supports a mitochondrial translation/charging theme.","confidence":"High","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0070158","count":5},{"id":"GO:0070150","count":5},{"id":"GO:0071897","count":5},{"id":"GO:0001701","count":5},{"id":"GO:0016260","count":5}]},{"hash":"278917397803818174","title":"Antibiotic Biosynthesis and Response","description":"This cluster shows a clear emphasis on antibiotic-related processes, with GO terms for antibiotic biosynthetic process and response to antibiotic both represented. While there are additional metabolic terms (nucleotide metabolism, PHB and riboflavin biosynthesis), the antibiotic-related terms provide the most specific thematic link among the proteins. Confidence is moderate due to the mix of other metabolic terms, but the antibiotic signal is compelling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0042619","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0019858","count":1}]},{"hash":"364380158059921789","title":"Oxidative stress response and redox detoxification","description":"The cluster is dominated by GO terms related to detoxifying cellular oxidants and maintaining redox balance (cellular oxidant detoxification; redox homeostasis) and stress-induced apoptotic signaling in response to oxidative stress, plus responses to UV and gamma radiation. This points to a core function in managing reactive oxygen species and DNA-damage signaling, with a few outlier terms touching adipocyte/mammary biology or general inflammatory regulation. Overall, redox regulation and oxidative stress response best explains the shared functions. ","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0098869","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0033599","count":1},{"id":"GO:0045444","count":1},{"id":"GO:0007605","count":1}]},{"hash":"2129564747982865357","title":"Ribosome biogenesis and RNA modification","description":"The cluster shows a strong signal for ribosome assembly and preribosome maturation (ribosome biogenesis, assembly of large subunit precursor of preribosome) along with multiple RNA modification processes (RNA methylation, guanine-N7 methylation, tRNA wobble cytosine methylation, mRNA capping). Although there is an outlier term (cobalamin biosynthesis), the dominant pattern ties to ribosome-related biogenesis and RNA processing, justifying this label.","confidence":"Medium","size":5,"edges":6,"triangles":2,"max_degree":4,"top_function":"protein-containing complex assembly","top_go_terms":[{"id":"GO:0009236","count":5},{"id":"GO:0006461","count":4},{"id":"GO:0042254","count":1},{"id":"GO:0018027","count":1},{"id":"GO:0009060","count":1}]},{"hash":"1891556165283848341","title":"Ubiquitin-Mediated Protein Quality Control","description":"The top terms cluster around ubiquitination and ER-associated degradation (ubiquitin-dependent ERAD, K63-linked ubiquitination, autoubiquitination) and include related protein folding/assembly regulation. This points to a cohesive role in marking and managing misfolded proteins via ubiquitin signaling and ERAD, with other terms likely reflecting broader stress responses rather than defining the core function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030433","count":3},{"id":"GO:0070534","count":2},{"id":"GO:0090035","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0071361","count":1}]},{"hash":"572531369664968977","title":"DNA replication and repair","description":"The cluster\u2019s GO terms are dominated by DNA replication, mitotic replication checkpoint signaling, and DNA damage repair (including UV-damage excision repair and translesion synthesis), suggesting a genome maintenance theme. Related terms on protein oligomerization/assembly likely reflect structural aspects of replication/repair complexes. Therefore, this label captures the core function of the cluster.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":3},{"id":"GO:0051260","count":2},{"id":"GO:0016562","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0034214","count":2}]},{"hash":"1745422238141232639","title":"Unknown","description":"The terms imply diverse regulatory roles across signaling, neural function, and chromatin, with no single shared process or strong interaction tying the proteins together, so a cohesive label cannot be assigned.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050821","count":1},{"id":"GO:0050808","count":1},{"id":"GO:0061051","count":1},{"id":"GO:0090263","count":1},{"id":"GO:0051085","count":1}]},{"hash":"1528139399964599248","title":"Embryonic and stem cell differentiation","description":"This cluster\u2019s top GO terms largely point to developmental processes and differentiation: erythrocyte development, mesodermal differentiation, blastocyst formation, and regulation of stem cell differentiation, along with epigenetic regulation of histone methylation. Although there are some plant-specific terms and obsolete annotations, the common theme is developmental progression and lineage specification, often tied to stem cell differentiation and early embryogenesis. Hence the label emphasizes embryonic development and stem cell regulation as the core theme.","confidence":"Medium","size":5,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0048821","count":2},{"id":"GO:0048333","count":2},{"id":"GO:1902465","count":2},{"id":"GO:2000736","count":2},{"id":"GO:2000864","count":2}]},{"hash":"406843790916711035","title":"Ubiquitin-mediated proteolysis","description":"This cluster is dominated by GO terms related to protein ubiquitination and ubiquitin-dependent degradation (ubiquitin-dependent protein catabolic process and ERAD-associated pathways), suggesting a core function in tagging and degrading proteins. A few terms point to extracellular matrix remodeling and immune-related processes, but the dominant, coherent signal centers on the ubiquitin-proteasome pathway.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016567","count":2},{"id":"GO:0033280","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0030433","count":2},{"id":"GO:0001913","count":1}]},{"hash":"86198475310427356","title":"Ribosome Biogenesis and Translation","description":"The cluster includes GO terms for translation (GO:0006412) and ribosomal large subunit assembly (GO:0000027), suggesting a ribosome-related core function. Several other terms point to oxidative stress or aging and may reflect noise or peripheral associations in this small cluster, but the presence of two core ribosome-related terms supports a label focused on ribosome biogenesis and protein synthesis. ","confidence":"Medium","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0001320","count":1},{"id":"GO:0019430","count":1},{"id":"GO:0010447","count":1},{"id":"GO:0001302","count":1}]},{"hash":"802819356720553988","title":"Unknown","description":"The GO terms for this cluster are highly diverse (cardiac communication, adipose differentiation, cell migration, NF-kappaB regulation, chemokine and inflammatory signaling, pain detection, hepatocyte apoptosis) with no edges connecting the proteins, making a coherent, representative theme unlikely to identify. Therefore this cluster is best labeled Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086070","count":2},{"id":"GO:1903444","count":2},{"id":"GO:0016477","count":2},{"id":"GO:0007253","count":2},{"id":"GO:0072660","count":2}]},{"hash":"2116975877505194531","title":"Translation-Linked signaling and endocytosis","description":"The strongest function is translation (GO:0006412), but several proteins also relate to phosphorylation (protein autophosphorylation) and membrane trafficking (endocytosis) with growth hormone signaling, suggesting a module where translation is coordinated with signaling and trafficking. Some nucleotide phosphorylation terms are obsolete and may reflect annotation noise.","confidence":"Medium","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0006186","count":1},{"id":"GO:0045920","count":1},{"id":"GO:0060416","count":1},{"id":"GO:0006187","count":1}]},{"hash":"1238795768988390739","title":"Ubiquitin-mediated protein quality control","description":"The top GO terms cluster around ubiquitination and proteostasis (K63-linked ubiquitination, autoubiquitination, ubiquitin-dependent ERAD pathway) and chaperone-assisted assembly, suggesting a shared function in tagging, degradation, and quality control of proteins. A few peripheral terms (ethanol response, apoptosis signaling) are less central and do not define the core theme.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090035","count":1},{"id":"GO:0070534","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0071361","count":1},{"id":"GO:0030579","count":1}]},{"hash":"1667356816497262162","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:1990417","count":3},{"id":"GO:0071035","count":3},{"id":"GO:0014070","count":3},{"id":"GO:1903608","count":3},{"id":"GO:0071051","count":3}]},{"hash":"2160229476796454164","title":"Unknown","description":"The GO terms mix chromatin-related regulation (histone acetylation, transcription start site selection, nucleosome density) with ribosome assembly (mitochondrial large subunit, ribosome assembly), plus other processes like post-transcriptional gene silencing and viral genome replication. This spread suggests no single cohesive function for the cluster, so a unified, intuitive label isn\u2019t justifiable. ","confidence":"","size":5,"edges":6,"triangles":2,"max_degree":3,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0071441","count":3},{"id":"GO:0001178","count":3},{"id":"GO:0060303","count":3},{"id":"GO:1902775","count":3},{"id":"GO:1904570","count":3}]},{"hash":"1615291248816871223","title":"Unknown","description":"The GO terms span diverse regulatory processes (GTPase activity regulation, ribophagy, synapse organization, nuclear/cytoplasmic transport regulation, ubiquitination, and more) with no single shared function across all proteins; thus a cohesive, specific label is not apparent.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0043547","count":2},{"id":"GO:0034517","count":1},{"id":"GO:0050808","count":1},{"id":"GO:0032443","count":1},{"id":"GO:2000238","count":1}]},{"hash":"850962063969436261","title":"Redox-immune signaling cluster","description":"This cluster appears driven by redox-related processes (cell redox homeostasis; removal of superoxide radicals) and immune signaling components (I-kappaB phosphorylation; regulation of non-canonical NF-kappaB signaling) with NK cell\u2013mediated cytotoxicity also represented, suggesting a link between oxidative stress responses and immune signaling. A few terms (lipoprotein biosynthesis, methylamine metabolism, spermatogenesis) seem less connected and likely reflect annotation noise. Overall, the theme centers on redox regulation intersecting immune signaling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0045454","count":2},{"id":"GO:0042158","count":1},{"id":"GO:0042267","count":1},{"id":"GO:0030416","count":1}]},{"hash":"341375527063820180","title":"Unknown","description":"The terms are scattered across xenobiotic catabolism, stress-related metabolic processes, and transcription/chromatin regulation (including some obsolete terms), with no clear unified function linking all proteins in this cluster.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046196","count":1},{"id":"GO:0009970","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0046306","count":1},{"id":"GO:0030961","count":1}]},{"hash":"141107558695178758","title":"Ribosome Biogenesis and Translation","description":"The cluster centers on translation and ribosome assembly/biogenesis, with multiple GO terms for ribosomal subunit assembly, preribosome maturation, and general translation processes (including termination). The presence of responses to antibiotics and cycloheximide indicates regulation linked to translation, supporting a theme of ribosome biogenesis coupled to translation control, despite a few outliers like iron homeostasis. Confidence: High","confidence":"","size":5,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":5},{"id":"GO:0046677","count":2},{"id":"GO:0090070","count":1},{"id":"GO:1902626","count":1},{"id":"GO:0046898","count":1}]},{"hash":"1344630400930960496","title":"NF-\u03baB\u2013Mediated Inflammatory Signaling","description":"This cluster is dominated by terms related to NF-\u03baB regulation (cytoplasmic sequestration and transcription factor activity) and chemokine production (MIP-1\u03b1, CCL5) with accompanying cell migration and inflammatory responses. While some terms touch on metabolism or apoptosis, the strongest, recurring theme is inflammation-associated signaling and immune chemokine regulation, suggesting a coherent inflammatory signaling cluster.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086070","count":4},{"id":"GO:1903444","count":4},{"id":"GO:0016477","count":4},{"id":"GO:0007253","count":4},{"id":"GO:0072660","count":4}]},{"hash":"1900619533756993811","title":"Unknown","description":"The proteins show a highly diverse set of GO terms (hormone biosynthesis regulation, erythrocyte differentiation, thiamine biosynthetic/metabolic processes, aging, stem cell proliferation, neuron maturation, histone methylation regulation, erythrocyte differentiation regulation, and camphor catabolism) with no obvious shared biological function. The term set is scattered across metabolism, development, and regulation, and there are no edges connecting the proteins, making a coherent label unlikely. ","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046886","count":3},{"id":"GO:0045648","count":3},{"id":"GO:0009228","count":3},{"id":"GO:0007568","count":3},{"id":"GO:2000648","count":3}]},{"hash":"358910852556005076","title":"NF-kB Signaling and Transcription Regulation","description":"Most terms point to regulation of transcription and signaling pathways affecting gene expression, especially NF-kappaB activation (I-kappaB phosphorylation, NIK) and transcriptional suppression, with supporting links to chromatin turnover and apoptosis. This suggests a cluster centered on transcriptional control intertwined with NF-kB signaling.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0036205","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0090073","count":1},{"id":"GO:1903721","count":1},{"id":"GO:0000122","count":1}]},{"hash":"289065038822043303","title":"Unknown","description":"The top GO terms cover several distinct themes: developmental processes in muscle and brain (skeletal muscle fiber development, substantia nigra development, cardiac muscle hypertrophy), vascular morphogenesis, and separate lipid/metabolism and xenobiotic response terms, plus a bacterial lipid A biosynthesis term. The lack of a single coherent function or pathway linking these terms makes it hard to assign a concise, meaningful label, so the cluster is best described as Unknown.","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":null,"top_go_terms":[{"id":"GO:0048741","count":2},{"id":"GO:0021762","count":2},{"id":"GO:0001569","count":1},{"id":"GO:0016576","count":1},{"id":"GO:0035690","count":1}]},{"hash":"2267836687537474128","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0048536","count":2},{"id":"GO:0042098","count":2},{"id":"GO:0016925","count":2},{"id":"GO:0090309","count":1},{"id":"GO:0061158","count":1}]},{"hash":"1015863382689956731","title":"Diverse Substrate Transmembrane Transporters","description":"The top GO terms cluster around transport across membranes for many substrates (nitrate, arabinose, urate, glucose transport in response to insulin, nitrite, sodium ions, trehalose, dehydroascorbic acid, etc.), indicating a group of transporter proteins with broad substrate range rather than a single substrate-specific function. The single outlying term on replicative senescence likely does not reflect the main function of the cluster. ","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":1},{"id":"GO:1904728","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0044381","count":1},{"id":"GO:0015747","count":1}]},{"hash":"1483675042608251666","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0000398","count":1},{"id":"GO:0080188","count":1},{"id":"GO:0009845","count":1},{"id":"GO:0000387","count":1},{"id":"GO:0000395","count":1}]},{"hash":"716831087382580277","title":"Mitotic Division and ER-Golgi Trafficking","description":"The cluster centers on mitotic processes (mitotic cell cycle, mitotic spindle assembly, cell division) and vesicle trafficking between the ER and Golgi (COPII-coated budding, retrograde transport). Growth and skeletal morphogenesis terms suggest developmental context, but the strongest signal is coordination between cell division and secretory pathway dynamics. Overall, the dominant theme is cell proliferation linked to ER-Golgi trafficking.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0035264","count":3},{"id":"GO:0008283","count":3},{"id":"GO:0090114","count":3},{"id":"GO:0006890","count":3},{"id":"GO:0000278","count":3}]},{"hash":"1842846439421188609","title":"Ubiquitin-Dependent Protein Turnover and Growth Regulation","description":"The dominant GO terms are about ubiquitination (autoubiquitination, polyubiquitination, ubiquitin-dependent degradation) and regulation of growth-related processes (cell cycle, organ growth, receptor turnover), indicating a cluster of proteins involved in ubiquitin-mediated protein turnover that modulates growth signals.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":5},{"id":"GO:0051865","count":5},{"id":"GO:0042787","count":5},{"id":"GO:0046621","count":5},{"id":"GO:0000209","count":5}]},{"hash":"1694410934760775584","title":"Spliceosome and Translation Machinery","description":"This cluster\u2019s top GO terms center on splicing (spliceosome conformational changes and catalytic assembly) and on various aspects of translation (cytoplasmic and mitochondrial translation, elongation, and a modification linked to translation). The common theme appears to be RNA processing coupled with protein synthesis machinery, suggesting these proteins function together in RNA maturation and translation contexts.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000388","count":1},{"id":"GO:1990416","count":1},{"id":"GO:2000767","count":1},{"id":"GO:0000349","count":1},{"id":"GO:0017183","count":1}]},{"hash":"1840755035879461656","title":"Unknown","description":"No shared GO terms or interactions are evident for these five proteins; Top Terms are empty, Edges are zero, and there is no clear common function to label. The note about 20 proteins re-added by ReCIPE does not provide a cohesive theme for the cluster.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"414936951547146674","title":"Calcium-cGMP signaling in heart and brain","description":"GO terms point to calcium release regulation, long-term potentiation, and guanylate cyclase activity, alongside heart development and vessel morphogenesis, suggesting a shared theme of calcium- and cGMP-mediated signaling in cardiovascular and neural contexts; the small, edge-free cluster makes this a cautious, moderate-confidence label.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001569","count":1},{"id":"GO:1901841","count":1},{"id":"GO:1900271","count":1},{"id":"GO:0060291","count":1},{"id":"GO:0007507","count":1}]},{"hash":"220425873294984804","title":"RNA Splicing and Translation Initiation","description":"The cluster is dominated by spliceosome-related terms (regulation of alternative splicing, splice site recognition, small-subunit processome assembly) alongside translation initiation terms (formation of translation preinitiation complex, eIF4F complex assembly). This suggests involvement in mRNA maturation and the assembly of the translation machinery, reflecting a cohesive role in post-transcriptional gene expression control. Some ncRNA- and miRNA-mediated silencing terms add a layer of RNA-based regulation that can intersect with splicing and translation control.","confidence":"High","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0016556","count":2},{"id":"GO:0001825","count":2},{"id":"GO:0031047","count":2},{"id":"GO:0035278","count":2}]},{"hash":"480716284868271731","title":"Heat-stress proteostasis and protein quality control","description":"The top GO terms converge on heat response, unfolded protein response, ER protein folding, and ubiquitin-proteasome\u2013mediated quality control, pointing to protein homeostasis under heat stress as the primary function of this cluster. Some terms like DNA replication and translational frameshifting are less central to this theme, but the dominant signal is proteostasis and quality control during heat stress.","confidence":"High","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":5},{"id":"GO:0006260","count":5},{"id":"GO:1900035","count":5},{"id":"GO:1901621","count":5},{"id":"GO:0034975","count":5}]},{"hash":"279562117546922762","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:1902570","count":2},{"id":"GO:1904751","count":1},{"id":"GO:0051096","count":1},{"id":"GO:0000390","count":1},{"id":"GO:0000381","count":1}]},{"hash":"117274373848562024","title":"Heat Stress and Protein Quality Control","description":"The enrichment centers on heat response, unfolded protein response, ER protein folding, and nuclear protein quality control by the ubiquitin-proteasome system, collectively indicating a cohesive proteostasis program active under heat stress. While a few terms relate to replication or signaling, the dominant theme across the cluster is protein folding and quality control mechanisms maintaining proteome integrity during stress.","confidence":"High","size":5,"edges":8,"triangles":5,"max_degree":4,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":4},{"id":"GO:0006260","count":4},{"id":"GO:1900035","count":4},{"id":"GO:1901621","count":4},{"id":"GO:0034975","count":4}]},{"hash":"1737685820397581798","title":"Mitotic spindle dynamics and chromosome segregation","description":"Most of the top GO terms describe mitotic processes and chromosome segregation: positive regulation of mitotic spindle elongation, chromosome passenger complex localization to spindle midzone, protein localization to kinetochore, and mitotic actomyosin contractile ring maturation, along with related phosphorylation/dephosphorylation controls. A few terms (mRNA capping, JNK regulation, and symbiont-mediated suppression of host IFN signaling) appear unrelated, likely reflecting general cellular processes or annotation noise in this small cluster. Overall, the cluster seems centered on mitosis and chromosome segregation dynamics.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902846","count":1},{"id":"GO:0006370","count":1},{"id":"GO:0031031","count":1},{"id":"GO:0044387","count":1},{"id":"GO:0039502","count":1}]},{"hash":"648787313461667677","title":"Platelet Activation and Coagulation Signaling","description":"The terms cluster around calcium-activated phospholipid scrambling (phosphatidylserine exposure), purinergic receptor signaling, and blood coagulation, which together point to platelet activation and membrane remodeling; bleb formation and ion transport further support this theme. A single term about insulin secretion is less directly connected, but the overall pattern best fits coagulation-related signaling.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045794","count":1},{"id":"GO:0035590","count":1},{"id":"GO:0061590","count":1},{"id":"GO:0061589","count":1},{"id":"GO:0007596","count":1}]},{"hash":"1862169843477200985","title":"Translational regulation and mRNA turnover","description":"The top terms cluster around translation processes (initiation, elongation, termination, and cytoplasmic translation) and mRNA decay (deadenylation-dependent decay), with selenocysteine incorporation linking to translation. This points to a translation-centric program with concurrent mRNA turnover.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":2},{"id":"GO:0000288","count":2},{"id":"GO:0006413","count":2},{"id":"GO:0006415","count":2},{"id":"GO:0014009","count":2}]},{"hash":"759353229760622296","title":"Seed coat mucilage and cell wall polysaccharide synthesis","description":"The top GO terms point to mucilage and pectin/hemicellulose biosynthesis (homogalacturonan, glucuronoxylan, poly-N-acetyllactosamine) and broader cell wall organization, along with plant-specific Hyp-O glycosylation of cell wall proteins, all of which together describe seed coat mucilage production and polysaccharide assembly in the cell wall.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010192","count":3},{"id":"GO:0010289","count":2},{"id":"GO:0018258","count":2},{"id":"GO:0048354","count":2},{"id":"GO:0007299","count":2}]},{"hash":"949163257433431231","title":"Mitochondrial Transport and Membrane Regulation","description":"The terms cluster around movement of substrates and ions across the mitochondrial membranes (ADP/ATP, alpha-ketoglutarate, Mg2+), and regulation of membrane permeability and potential. Additional signals relate to cellular energy and stress responses (insulin signaling and response to superoxide). Together they indicate a mitochondrial transport/regulatory module.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":1},{"id":"GO:0051881","count":1},{"id":"GO:0015742","count":1},{"id":"GO:0032869","count":1},{"id":"GO:1990314","count":1}]},{"hash":"1139867285333809671","title":"Unknown","description":"The terms span plant hormone signaling (gibberellin, ABA), development (trichome patterning), DNA repair and telomere/chromatin dynamics, and RNA transcription/localization, with no clear shared function linking these proteins.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009739","count":1},{"id":"GO:1900033","count":1},{"id":"GO:1990414","count":1},{"id":"GO:1905778","count":1},{"id":"GO:0016032","count":1}]},{"hash":"228589577312211590","title":"Zinc Ion Transport and Homeostasis","description":"This cluster is dominated by GO terms related to zinc handling: import of zinc ions across the plasma membrane, intracellular zinc ion homeostasis, detoxification of zinc ions, and cellular response to zinc ion starvation, pointing to a cohesive role in zinc acquisition and regulation. A single outlier term on limb development appears incidental, and the lack of edges suggests these proteins may share function without direct interactions in this dataset. Overall, the set is best described as zinc ion transport and homeostasis-related proteins.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010312","count":1},{"id":"GO:0006831","count":1},{"id":"GO:0006830","count":1},{"id":"GO:0034224","count":1},{"id":"GO:0070574","count":1}]},{"hash":"329401388510769750","title":"Unknown","description":"The terms span multiple, distinct processes (sulfur and chlorophyll metabolism, various stress responses, DNA and protein repair, nitric oxide biosynthesis, and even viral mRNA export) with no clear shared function or pathway. The cluster has no edges, suggesting little direct connectivity, so a single, representative label cannot be confidently assigned. ","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006790","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0015994","count":1},{"id":"GO:1901530","count":1},{"id":"GO:0010477","count":1}]},{"hash":"905943022683644301","title":"Diverse biosynthesis and modification pathways","description":"This cluster shows a mix of biosynthetic processes (homogalacturonan/polysaccharide, antibiotic, biotin, polyamine, vitamin E biosynthesis) and various RNA/protein modification activities (RNA guanine-N7 methylation, 7-methylguanosine mRNA capping, peptidyl-lysine dimethylation), plus a metabolic process (aerobic respiration) and xenobiotic response. The common thread is involvement in biosynthetic or modification pathways rather than a single defined function, so a broad label like \"Diverse biosynthesis and modification pathways\" best captures the cluster.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010289","count":2},{"id":"GO:0036265","count":2},{"id":"GO:0017000","count":2},{"id":"GO:0018027","count":1},{"id":"GO:0009060","count":1}]},{"hash":"682500916354172579","title":"Heat Stress Response and Transcriptional Regulation","description":"The cluster\u2019s GO terms cluster around heat response and protein folding (response to heat; protein folding in ER), indicating a heat-shock\u2013related maintenance of proteostasis. Supporting terms\u2014DNA replication and cell cycle\u2014suggest these proteins may also participate in cell-cycle/transcriptional adjustments during stress, with positive regulation of RNA polymerase II\u2013mediated transcription tying in transcriptional control under heat. The mix points to a cohesive theme of heat-stress management coupled with transcriptional and replication coordination, albeit with some noise from less central terms.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":2},{"id":"GO:0006260","count":2},{"id":"GO:0007049","count":2},{"id":"GO:0035640","count":2},{"id":"GO:0045944","count":2}]},{"hash":"485067208570405784","title":"Unknown","description":"The terms span diverse biological processes\u2014from RNA processing and DNA replication to cofactor biosynthesis and even fungal cell wall biosynthesis and regulatory signaling\u2014without a single cohesive function tying all members together. This appears to be a mixed collection rather than a unified functional module, so I cannot assign a specific, representative label beyond Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030488","count":1},{"id":"GO:0006364","count":1},{"id":"GO:0009236","count":1},{"id":"GO:0006479","count":1},{"id":"GO:0070389","count":1}]},{"hash":"1328354454454290110","title":"Mitochondrial dynamics and membrane trafficking","description":"The top GO terms place strong emphasis on mitochondrial processes (fission, membrane organization, inheritance, and intracellular distribution), suggesting a core role in mitochondrial dynamics. Additional terms point to membrane trafficking and signaling (endocytic recycling, ephrin receptor signaling, and GABAergic synaptic transmission), which may reflect context-specific or multifunctional roles. Overall, the dominant theme is mitochondrial dynamics with related membrane trafficking activities.","confidence":"Medium","size":5,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0090307","count":2},{"id":"GO:0032456","count":2},{"id":"GO:0048013","count":2},{"id":"GO:0051932","count":2},{"id":"GO:0000266","count":2}]},{"hash":"641321956783075167","title":"Fatty acid biosynthesis","description":"Based on GO terms, two terms are fatty acid biosynthetic process and long-chain fatty-acyl-CoA metabolic process, each with 2 proteins, suggesting a lipid-synthetic function among the cluster. The remaining terms are sparse and cover diverse processes (protein export, insulin response, keratinization, neuron migration, mitochondria cytochrome c release, synaptic plasticity) that do not coherently define a single pathway; thus the main theme is fatty acid metabolism, with some noise.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006633","count":2},{"id":"GO:0035336","count":2},{"id":"GO:0046827","count":1},{"id":"GO:1902309","count":1},{"id":"GO:0006605","count":1}]},{"hash":"870567509063066535","title":"Diverse Biosynthetic Pathways","description":"Top GO terms are dominated by biosynthetic processes (antibiotic biosynthesis, glucocorticoid biosynthesis, melanin biosynthesis, mycolic acid biosynthesis, fatty acid elongation), implying a general theme of metabolite production. A few terms\u2014such as lung development and regulation of DNA-templated transcription\u2014do not fit this theme, suggesting the cluster is heterogeneous. Therefore, label as Diverse Biosynthetic Pathways.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":3},{"id":"GO:0008209","count":2},{"id":"GO:0006355","count":2},{"id":"GO:0006710","count":2},{"id":"GO:0030324","count":2}]},{"hash":"1822672239483842207","title":"Skeletal Muscle Ion Transport and T-tubule Organization","description":"This cluster is dominated by GO terms for ion homeostasis and transport (manganese, potassium, copper, sodium) across membranes, which points to ion balance mechanisms. The presence of terms related to fast-twitch muscle fiber contraction and T-tubule organization suggests a muscle-specific context, likely reflecting proteins involved in excitation-contraction coupling and ion handling in skeletal muscle. While some heart-related regulatory terms appear, the core signal centers on muscle ion transport and organization patterns.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030026","count":3},{"id":"GO:0006813","count":2},{"id":"GO:1901205","count":2},{"id":"GO:1990938","count":2},{"id":"GO:0060003","count":2}]},{"hash":"157658553924928963","title":"Lung and vascular development","description":"Top GO terms are dominated by lung development and branching involved in blood vessel morphogenesis, suggesting a developmental program for respiratory and vascular tissues. While there are secondary terms related to lipid metabolism and vesicle transport, they do not form a tight cohesive theme with the development signals. Overall, the most representative label is \"Lung and vascular development.\"","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030324","count":3},{"id":"GO:0001569","count":2},{"id":"GO:0016576","count":2},{"id":"GO:0035690","count":2},{"id":"GO:1900486","count":2}]},{"hash":"194190580501600013","title":"Diverse biosynthesis: sugars and lipids","description":"The GO terms show multiple biosynthetic processes across carbohydrates (starch, glucose, sucrose) and lipids (phospholipids, glycolipids, GPI anchors), plus bacillithiol biosynthesis, suggesting a broad biosynthetic/metabolic theme rather than a single precise function. A couple terms like feeding behavior and response to mannitol are peripheral, but do not override the core biosynthesis signal.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0019252","count":2},{"id":"GO:0005985","count":2},{"id":"GO:0071793","count":2},{"id":"GO:0006006","count":2},{"id":"GO:0008654","count":2}]},{"hash":"273784442615232689","title":"Unknown","description":"The GO terms are highly diverse and include plant hormone response (strigolactone), lipid metabolism (phospholipid dephosphorylation, monoacylglycerol catabolic), amino acid biosynthesis/activation, xenobiotic and obsolete annotations, and signaling regulation. With only five proteins and no cohesive, single-function theme across these terms, there isn\u2019t a reliable, specific label that captures the cluster\u2019s common function. ","confidence":"","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046939","count":1},{"id":"GO:1902348","count":1},{"id":"GO:0019260","count":1},{"id":"GO:0043041","count":1},{"id":"GO:0009086","count":1}]},{"hash":"1071392361202840141","title":"Terpenoid and sterol biosynthesis","description":"This cluster is dominated by GO terms for terpenoid/isoprenoid biosynthesis (monoterpene; farnesyl, geranyl, and geranylgeranyl diphosphate biosynthesis) and cholesterol biosynthesis, pointing to a common function in isoprenoid/sterol production. Some terms like virion assembly and protein transport appear but are less central and likely represent broader cellular processes or noise. Overall, the main theme is terpenoid/sterol biosynthesis among the proteins.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0043693","count":1},{"id":"GO:0006695","count":1},{"id":"GO:0051290","count":1},{"id":"GO:0015031","count":1},{"id":"GO:1901663","count":1}]},{"hash":"954306237844596846","title":"Plant cell wall glycoprotein biosynthesis","description":"These proteins are tied to plant extracellular matrix components, especially arabinogalactan proteins (AGPs) and their O-linked glycosylation, as well as glycans involved in seed mucilage and root hair development. The GO terms show AGP metabolic processes, Hyp-O-glycosylation, mucilage biosynthesis, and root hair development, pointing to a cohesive theme of AGP-rich cell wall glycoprotein biosynthesis, with a few terms likely representing cross-species or broad annotations. Confidence: High","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0075015","count":3},{"id":"GO:0080147","count":3},{"id":"GO:0030311","count":2},{"id":"GO:0042248","count":2},{"id":"GO:0010405","count":2}]},{"hash":"110785011002039642","title":"Cardiovascular Signaling and Platelet Activation","description":"The terms cluster around heart development, VEGF-driven vascular signaling, integrin activation/adhesion, and platelet activation, with additional hints of secretory processes (dense core granule exocytosis, catecholamine secretion) that can influence vascular function. This suggests a cohesive theme of cardiovascular signaling and cell adhesion/activation, rather than a single isolated pathway, hence the label.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0033623","count":1},{"id":"GO:0007507","count":1},{"id":"GO:0016477","count":1},{"id":"GO:0033622","count":1},{"id":"GO:1990504","count":1}]},{"hash":"2054685034674828624","title":"Diverse Metabolic Pathways","description":"The GO terms cover a range of biosynthetic and metabolic activities (biotin biosynthesis, lysine biosynthesis via aminoadipic acid, protoporphyrinogen IX biosynthesis, antibiotic biosynthesis, kynurenic acid biosynthesis) plus metabolic regulation and lipid handling (cellular response to insulin, fatty acid transport and homeostasis) and catabolic steps (aspartate and alanine catabolism). This spread indicates the proteins participate in multiple metabolic processes rather than a single pathway, so a general \"Diverse Metabolic Pathways\" label fits best.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009102","count":3},{"id":"GO:0019878","count":3},{"id":"GO:0006782","count":3},{"id":"GO:0017000","count":2},{"id":"GO:0034276","count":2}]},{"hash":"1435208091697029698","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":3},{"id":"GO:0033358","count":2},{"id":"GO:0009718","count":2},{"id":"GO:0042351","count":2},{"id":"GO:0080110","count":2}]},{"hash":"92053258178174352","title":"ER Protein Folding and Oxidative Stress Response","description":"Top GO terms indicate ER-associated functions: protein folding in the endoplasmic reticulum, ER stress response, and oxidative stress/detoxification, suggesting a cluster of proteins involved in ER quality control and redox homeostasis.","confidence":"High","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033158","count":1},{"id":"GO:0034599","count":1},{"id":"GO:0018401","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0098869","count":1}]},{"hash":"834839049553744532","title":"Unknown","description":"The top GO terms span spermatid and wing/eye cell fate specification, EGFR ligand maturation, unfolded protein response, ER-to-cytosol proteolysis, and organelle contact (mitochondrion-ER tethering), plus neuronal spine morphogenesis and spindle pole protein localization. This mix shows no single cohesive biological theme or pathway tying all proteins together, suggesting the cluster is compositionally heterogeneous rather than functionally cohesive. Degree is zero, and there are no apparent interactions within the cluster, supporting an Unknown label. ","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048515","count":2},{"id":"GO:1904211","count":2},{"id":"GO:0038005","count":2},{"id":"GO:0034620","count":2},{"id":"GO:0032815","count":2}]},{"hash":"2292265832739757456","title":"Splicing and Translation Initiation Regulation","description":"These proteins cluster around RNA processing and control of gene expression at the post-transcriptional level, with strong representation of splicing (spliceosome regulation, splice site recognition, small-subunit processome), mRNA processing and stabilization, and initiation of translation (eIF4F complex assembly, preinitiation complex formation). The presence of regulatory ncRNA- and miRNA-mediated silencing further supports a theme of RNA-based regulation. The blastocyst formation term may reflect developmental contexts where these processes are coordinated. Overall, a cohesive RNA processing/translation-regulation cluster.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0000381","count":3},{"id":"GO:0016556","count":3},{"id":"GO:0001825","count":3},{"id":"GO:0031047","count":3},{"id":"GO:0035278","count":3}]},{"hash":"1672970829536670048","title":"Unknown","description":"No GO terms are provided to define a shared function, so a meaningful label cannot be assigned. The absence of functional terms prevents identifying a cohesive theme for this small cluster.","confidence":"","size":5,"edges":5,"triangles":1,"max_degree":4,"top_function":null,"top_go_terms":[]},{"hash":"356341731814445184","title":"Antibiotic degradation and nylon catabolic enzymes","description":"The top GO terms cluster around beta-lactam antibiotic catabolic process, general antibiotic response, and nylon catabolic process, plus regulation of beta-lactamase activity. This pattern points to a set of enzymes involved in degrading antibiotics (especially beta-lactams) and nylon-like substrates, possibly beta-lactamase or nylonase\u2013type activities. Some unrelated terms appear (heat response, DNA replication, folding, frameshifting), but they don\u2019t override the core theme. Overall, the cluster appears to reflect a shared function in antibiotic and nylon degradation.","confidence":"Medium","size":5,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0030655","count":2},{"id":"GO:0046677","count":2},{"id":"GO:0019876","count":2},{"id":"GO:0033252","count":2},{"id":"GO:0009408","count":1}]},{"hash":"1348331884823522475","title":"Neuronal polarity and dendritic spine morphogenesis","description":"The frequent GO terms center on neural cell polarity, dendritic spine morphogenesis, and organized trafficking processes (ER-Golgi transport, mitochondrion-ER tethering). This points to a cohesive theme around neuronal morphology and polarized protein/vesicle trafficking, even though some terms relate to broader cell-polarity and trafficking mechanics, suggesting a representative neuronal development module.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0061001","count":2},{"id":"GO:1990456","count":2},{"id":"GO:1902542","count":2},{"id":"GO:0034332","count":2},{"id":"GO:0032878","count":2}]},{"hash":"813458606872750492","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031119","count":2},{"id":"GO:0090669","count":1},{"id":"GO:0000495","count":1},{"id":"GO:0031120","count":1},{"id":"GO:0031118","count":1}]},{"hash":"1393035067965275361","title":"Membrane Transporters and Xenobiotic Export","description":"GO terms center on transport across membranes and export/import of xenobiotics and related molecules (xenobiotic export from cell, daunorubicin transport, taurine transmembrane transport, oligopeptide export from mitochondrion, teichoic acid transport, ceramide translocation, long-chain fatty acid import into peroxisome). This pattern strongly suggests a cluster of membrane transporters or transport-related proteins; one outlier term (nucleotide-excision repair) may reflect annotation noise rather than the core function.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046618","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0015910","count":2},{"id":"GO:0015777","count":2},{"id":"GO:0043213","count":2}]},{"hash":"901966624622889041","title":"TLR-Mediated antiviral innate immune signaling","description":"The terms highlight TLR7/8 signaling, MyD88-dependent TLR signaling, interferon-\u03b1 production, and innate immune defense against viruses, which together define an antiviral innate immune signaling cluster. A few non-immune terms (mitochondrial permeability/regulation, metabolism) appear but are not central to the main theme. Therefore, the label reflects the core function.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034158","count":2},{"id":"GO:0002755","count":2},{"id":"GO:0045356","count":2},{"id":"GO:0045087","count":2},{"id":"GO:0034154","count":2}]},{"hash":"676914223684008203","title":"Unknown","description":"The top GO terms are too disparate to form a single coherent function for the cluster: a general carbohydrate metabolic process, a plant-specific phytochelatin biosynthetic process, regulation of autophagy and catalytic activity, and proteolysis. With only one representative term per category and no clear shared pathway, there isn\u2019t a single representative function to name the cluster.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0005975","count":1},{"id":"GO:0046938","count":1},{"id":"GO:1904715","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0043085","count":1}]},{"hash":"2293342976985831969","title":"Mitochondrial ion and metabolite transport","description":"The cluster is dominated by transport of ions (manganese, magnesium, ADP/ATP) and a key metabolite (alpha-ketoglutarate) across mitochondrial membranes, along with regulation of membrane potential and permeability. This points to a cohesive theme of mitochondrial transport and energy regulation, with additional signals linking to metabolic regulation (insulin/IGF) and oxidative stress response.","confidence":"High","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006828","count":2},{"id":"GO:0046902","count":1},{"id":"GO:0051881","count":1},{"id":"GO:0015742","count":1},{"id":"GO:0032869","count":1}]},{"hash":"1204061765397084602","title":"Triglyceride Catabolism and Phospholipid Remodeling","description":"This cluster is dominated by GO terms describing triglyceride catabolic processes, triglyceride mobilization, and remodeling of phospholipids (phosphatidylcholine and phosphatidylethanolamine). The consistent lipid-centric terms suggest proteins involved in lipid breakdown and membrane lipid remodeling. A single outlier term (cell budding) is minor and does not alter the overarching theme. The connection to negative regulation of PKA activity may reflect signaling control of lipid metabolism, reinforcing the lipid-focused theme.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010898","count":5},{"id":"GO:0034638","count":5},{"id":"GO:0019433","count":5},{"id":"GO:0036153","count":5},{"id":"GO:0046338","count":5}]},{"hash":"1098826686470572124","title":"Ribosome Biogenesis and Septin-Cytokinesis Machinery","description":"The GO terms cluster around ribosome production and function (biogenesis, export, cytoplasmic translation) alongside septin ring organization/assembly and cytokinesis-related processes (division septum, spindle assembly), suggesting a combined role in growth-related protein synthesis and septin-driven cell division. This supports a cohesive theme of ribosome biogenesis linked to cytokinetic/septin machinery.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0000917","count":1},{"id":"GO:0007056","count":1},{"id":"GO:0032186","count":1},{"id":"GO:0000055","count":1}]},{"hash":"1244736669522101925","title":"Glycolysis and fructose metabolism","description":"The top GO terms strongly point to core glycolytic processes, including canonical glycolysis, fructose 1,6-bisphosphate metabolism, and fructose catabolism to glyceraldehyde-3-phosphate and dihydroxyacetone phosphate. Additional terms suggest energy-related regulation and protein assembly, with a weaker link to oxygen-sensing/prolyl hydroxylation pathways. Overall, the cluster appears to group enzymes and regulators involved in glycolysis and related energy production processes.","confidence":"Medium","size":5,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0018401","count":1},{"id":"GO:1901874","count":1},{"id":"GO:0032364","count":1},{"id":"GO:0061621","count":1}]},{"hash":"245952162677697532","title":"Unknown","description":"The top terms are a scattered mix of diverse metabolic and biosynthetic processes (various catabolic processes, catecholamine metabolism, cobalamin and lignin biosynthesis, protein methylation, and hormone biosynthesis regulation) with several obsolete terms, and no single coherent pathway or function ties all proteins together. This makes it impractical to assign a specific, representative label beyond Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042135","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0019629","count":1},{"id":"GO:0019396","count":1},{"id":"GO:0009236","count":1}]},{"hash":"787999700901042314","title":"Unknown","description":"The top GO terms cover a mix of metabolic processes (thiamine biosynthesis, mitochondrial electron transport) and various developmental/regulatory processes (erythrocyte/megakaryocyte differentiation, embryonic development) with several terms marked obsolete. There isn\u2019t a clear, single biological function or pathway tying these proteins together, suggesting either diverse roles or noise in the annotation. ","confidence":"","size":5,"edges":3,"triangles":0,"max_degree":2,"top_function":"regulation of DNA-templated transcription","top_go_terms":[{"id":"GO:0009228","count":5},{"id":"GO:0010725","count":5},{"id":"GO:0014063","count":5},{"id":"GO:0043046","count":5},{"id":"GO:0006120","count":5}]},{"hash":"815516707224206372","title":"Unknown","description":"The top GO terms cover a mix of developmental morphogenesis (optic nerve, corpus callosum, lung mesenchyme), cell migration, immune signaling, and stress/response processes, with no single dominant function tying the cluster together.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":1},{"id":"GO:0010898","count":1},{"id":"GO:0060484","count":1},{"id":"GO:0022038","count":1},{"id":"GO:0050853","count":1}]},{"hash":"1708289750888068880","title":"Unknown","description":"The top GO terms are highly diverse, including insulin secretion, regulation of activin signaling, cardiac tissue morphogenesis, neuronal signaling, redox/oxidative stress responses, histone isomerization, hydrogen peroxide response, and cell division. With no edges or coherent clustering among these functions, there isn\u2019t a single shared biological theme to bind the proteins together. Therefore, assign Unknown.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030073","count":1},{"id":"GO:0032925","count":1},{"id":"GO:1901710","count":1},{"id":"GO:0055010","count":1},{"id":"GO:0051775","count":1}]},{"hash":"597129257476267191","title":"ER-associated protein quality control and degradation","description":"This cluster shows strong enrichment for ERAD-related and ubiquitin-proteasome\u2013mediated quality control terms, including ER-to-cytosol retrograde transport, cytoplasm protein quality control, and ribosome-associated degradation. The presence of nonfunctional rRNA decay and ribosome quality control terms reinforces the theme of cellular surveillance and clearance of defective translation products. Collectively, the proteins appear to function in ER-associated degradation and related proteostatic pathways.","confidence":"High","size":5,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070651","count":1},{"id":"GO:0030970","count":1},{"id":"GO:0051974","count":1},{"id":"GO:1990116","count":1},{"id":"GO:0071712","count":1}]},{"hash":"1014708888208108250","title":"Unknown","description":"Unknown","confidence":"","size":5,"edges":10,"triangles":10,"max_degree":4,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:1903608","count":5},{"id":"GO:1902775","count":5},{"id":"GO:1904570","count":5},{"id":"GO:0042255","count":5},{"id":"GO:0016441","count":5}]},{"hash":"1263045692090024436","title":"Cardiac Muscle Development and Calcium Signaling","description":"The top GO terms point to ventricular heart tissue morphogenesis, heart development, and regulation of calcium signaling and calcium-release channels, all suggesting proteins involved in cardiac muscle differentiation and excitation-contraction coupling. While a few terms touch neural signaling, the dominant theme is cardiac development and calcium handling pathways.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055010","count":3},{"id":"GO:0060315","count":3},{"id":"GO:0006469","count":3},{"id":"GO:0001569","count":2},{"id":"GO:1901841","count":2}]},{"hash":"490304676226849928","title":"Unknown","description":"The top GO terms span fungal sporulation, vertebrate development (heart and blood vessels), neuronal signaling (long-term potentiation, calcium regulation), and non-autophagic vacuole fusion, with no single shared function across all proteins. Several terms are obsolete as well, so there is no coherent functional theme to assign a specific label.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0031954","count":3},{"id":"GO:0030437","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0042144","count":3},{"id":"GO:0001569","count":2}]},{"hash":"1434453009571676678","title":"ER Stress and Unfolded Protein Response","description":"The cluster shows enrichment for unfolded protein response, cellular response to unfolded protein, and ER-stress\u2013related regulation, pointing to a function in protein-folding quality control and ER homeostasis. Some unrelated terms (iron-sulfur cluster assembly, beta-glucan biosynthesis, DNA replication) suggest noise or multifunctionality, so the core theme is present but not uniformly represented.","confidence":"Medium","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0070389","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0070880","count":1},{"id":"GO:1903382","count":1},{"id":"GO:1902037","count":1}]},{"hash":"2224167307283176667","title":"Unknown","description":"The GO terms include nervous system development (optic nerve morphogenesis, corpus callosum development), mesenchyme/lung development, cell migration, apoptosis regulation, B cell receptor signaling, and stress/virus responses. The diversity and lack of a shared pathway, plus no edges between proteins, suggest there is no single cohesive function to label this cluster with a specific, intuitive function. ","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016477","count":1},{"id":"GO:0010898","count":1},{"id":"GO:0060484","count":1},{"id":"GO:0022038","count":1},{"id":"GO:0050853","count":1}]},{"hash":"1807501198013978512","title":"Protein acetylation processes","description":"The top GO terms are dominated by acetylation-related annotations (N-terminal acetylation, peptidyl-lysine acetylation, spermine and histone acetylation, N-terminal propionylation, etc.), with some related catabolic processes that use acetyl groups. This suggests the cluster centers on acetylation modifications and their metabolism rather than a single substrate, hence the label.","confidence":"High","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009447","count":5},{"id":"GO:0018003","count":5},{"id":"GO:2000025","count":5},{"id":"GO:0006044","count":5},{"id":"GO:0032919","count":5}]},{"hash":"512195596957766663","title":"Unknown","description":"The GO terms span diverse processes across organelles (mitochondria, chloroplasts) and metabolism with no single unifying function, making a concise, representative label inappropriate. Therefore a default Unknown with no clear theme is most appropriate.","confidence":"","size":5,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035690","count":1},{"id":"GO:0030308","count":1},{"id":"GO:0061668","count":1},{"id":"GO:0009658","count":1},{"id":"GO:0006390","count":1}]},{"hash":"1592477554109046131","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"autophagy","top_go_terms":[{"id":"GO:0051865","count":4},{"id":"GO:0030433","count":4},{"id":"GO:0070534","count":4},{"id":"GO:0036205","count":3},{"id":"GO:0048536","count":3}]},{"hash":"1159085189049038429","title":"Cellular stress response and protein folding","description":"The top GO terms cluster around stress-induced regulation of proteins\u2014response to heat and ischemia, ATP response, protein stabilization, and chaperone-mediated folding/refolding\u2014pointing to cellular proteostasis under stress. Some terms (virion assembly, TNF signaling) are outliers, but the dominant theme is stress response and protein homeostasis.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":4},{"id":"GO:0050821","count":4},{"id":"GO:0019068","count":4},{"id":"GO:0051086","count":4},{"id":"GO:0033198","count":4}]},{"hash":"223161363324013486","title":"Actin-dependent vesicle trafficking and cell migration","description":"The terms strongly cluster around actin dynamics (positive regulation of actin nucleation, vesicle transport along actin filaments, cell gliding, VEGF-driven cell migration) and adjacent membrane/secretory processes (plasma membrane raft distribution, secretory granule localization, Fc-gamma receptor signaling in phagocytosis). This suggests a shared function in actin-driven movement and vesicle trafficking at the cell surface.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0044855","count":1},{"id":"GO:0031585","count":1},{"id":"GO:0030050","count":1},{"id":"GO:0038089","count":1},{"id":"GO:0051127","count":1}]},{"hash":"1185724670726749342","title":"Ubiquitin-Dependent Protein Turnover and Signaling","description":"The cluster\u2019s top GO terms cluster around ubiquitin-mediated regulation: ubiquitin-dependent protein catabolic process, protein autoubiquitination, K63-linked ubiquitination, ribophagy, and regulation of JNK cascade, with supporting signals from apoptotic processes. While a couple terms touch on developmental processes, the strongest cohesive theme is ubiquitin-driven control of protein turnover and stress signaling pathways.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046328","count":2},{"id":"GO:0060575","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0060669","count":2},{"id":"GO:0045944","count":2}]},{"hash":"361276048817634035","title":"Unknown","description":"The top GO terms are spread across lipid metabolism (carnitine metabolic process, cholesterol biosynthetic process, hydrogen sulfide biosynthesis), ion transport (sodium ion transport), signaling and immune modulation (positive regulation of guanylate cyclase activity, interleukin-6 production), and endothelial development regulation, with only a single edge and no clear single function linking all terms. This scattered functional profile makes it hard to assign a coherent, specific label, so Unknown is appropriate here.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009437","count":2},{"id":"GO:0006695","count":1},{"id":"GO:0010124","count":1},{"id":"GO:0032770","count":1},{"id":"GO:0006814","count":1}]},{"hash":"1131504205068421901","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0071320","count":2},{"id":"GO:0006207","count":2},{"id":"GO:0044205","count":2},{"id":"GO:0090038","count":1},{"id":"GO:0009627","count":1}]},{"hash":"207123874218020551","title":"Diverse regulatory cellular processes","description":"This cluster shows a mix of GO terms centered on regulation across multiple domains\u2014signaling (Wnt, Hippo), differentiation (keratinocyte, muscle), apoptotic control, and regulation of various biosynthetic and cellular activities (ribophagy, tRNA export, synapse organization). There is no single cohesive pathway or process, suggesting proteins involved in broad regulatory roles rather than one specific function.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0060044","count":3},{"id":"GO:0030216","count":3},{"id":"GO:0090263","count":3},{"id":"GO:0035329","count":3},{"id":"GO:0006915","count":3}]},{"hash":"1656823901783591606","title":"Mitotic spindle and microtubule dynamics","description":"GO terms predominantly describe microtubule-based processes relevant to mitosis and spindle function, including plus-end microtubule depolymerization, spindle midzone assembly, mitotic metaphase chromosome recapture, regulation of microtubule-based processes, and plus-end\u2013directed vesicle transport along microtubules. This indicates a coherent theme of microtubule dynamics during cell division, with a couple of peripheral terms (Rap signaling, chloroplast movement) that may reflect broader cytoskeletal regulation.","confidence":"High","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0032487","count":4},{"id":"GO:0001560","count":4},{"id":"GO:0070462","count":4},{"id":"GO:0009904","count":4},{"id":"GO:1990942","count":4}]},{"hash":"78649825901534719","title":"Fe-S cluster biosynthesis and nitrogen fixation","description":"Most of the top GO terms point to iron-sulfur cluster assembly (GO:0016226) and nitrogen fixation (GO:0009399), suggesting proteins involved in Fe-S biogenesis necessary for nitrogenase maturation. Additional terms like protein maturation and various hydroxylation processes may reflect broader processing roles, while the cellular response to exogenous dsRNA appears unrelated to the core theme and could be annotation noise. Overall, the cluster is best described by Fe-S cluster biosynthesis and nitrogen fixation functions.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071360","count":2},{"id":"GO:0051604","count":1},{"id":"GO:0009399","count":1},{"id":"GO:0016226","count":1},{"id":"GO:0006880","count":1}]},{"hash":"1917449172238802531","title":"Ubiquitination and Proteostasis Regulation","description":"The top GO terms are dominated by ubiquitin-related processes (K63-linked ubiquitination, autoubiquitination, and ubiquitin-dependent ERAD) and a link to chaperone-mediated protein assembly, pointing to a theme of ubiquitin-driven proteostasis and protein quality control. While some terms touch on stress or immune signaling, the strongest and most coherent signal across the cluster is ubiquitin modification and proteostasis regulation.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090035","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0071361","count":2},{"id":"GO:0030579","count":2}]},{"hash":"1855029562828305833","title":"Heat stress proteostasis and ER folding","description":"This cluster features GO terms for response to heat, unfolded protein response, ER protein folding, and proteasome-mediated quality control, indicating a cohesive module focused on maintaining proteome integrity under heat stress; other terms appear incidental rather than defining the core function.","confidence":"High","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1900035","count":3},{"id":"GO:1901621","count":3},{"id":"GO:0034975","count":3}]},{"hash":"749457645014436348","title":"Nucleotide metabolism and salvage","description":"The top GO terms cluster around nucleotide metabolism and biosynthesis (ADP/CDP formation, nucleoside monophosphate phosphorylation, AMP salvage, purine ribonucleotide interconversion), pointing to enzymes involved in nucleotide production and recycling. A couple of terms for brain and liver development likely reflect tissue-specific expression rather than main function. Overall, the common theme is nucleotide metabolism and salvage.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046939","count":2},{"id":"GO:0007420","count":2},{"id":"GO:0046041","count":2},{"id":"GO:0006172","count":2},{"id":"GO:0046940","count":2}]},{"hash":"1625907114591060044","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071157","count":1},{"id":"GO:0034121","count":1},{"id":"GO:0000122","count":1},{"id":"GO:0043066","count":1},{"id":"GO:0000209","count":1}]},{"hash":"2266943223239568459","title":"Diverse Metabolic Processes","description":"The top GO terms cover a range of metabolic activities\u2014from uracil and creatinine catabolism to nicotinamide/nicotinate metabolism and nitrogen utilization\u2014along with some xenobiotic degradation and signaling/age-related terms. This suggests the cluster comprises proteins involved in various, loosely connected metabolic pathways rather than a single, unified function. The lack of edges also indicates these proteins may operate in different contexts or processes. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006212","count":2},{"id":"GO:0002047","count":1},{"id":"GO:0019358","count":1},{"id":"GO:0001302","count":1},{"id":"GO:0006769","count":1}]},{"hash":"1483358035375697515","title":"Unknown","description":"The GO terms are highly heterogeneous, including nitrate assimilation/transport, mitochondrial inheritance, and several unrelated processes (sebaceous gland differentiation, CNS myelin maintenance, sterol and sphingolipid metabolism). There isn\u2019t a clear, shared biological theme across the cluster, so a specific, representative label isn\u2019t evident.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042128","count":2},{"id":"GO:0000001","count":2},{"id":"GO:0001949","count":1},{"id":"GO:0006675","count":1},{"id":"GO:0032443","count":1}]},{"hash":"967645318756984326","title":"Unknown","description":"The top GO terms span diverse, unrelated processes (reproduction like acrosome assembly and spermatid differentiation; plant-specific floral organ abscission; vesicle trafficking via COPI; lysosomal membrane organization; ion transport; apoptosis; cell migration). With no edges connecting the proteins and no clear shared function, there isn\u2019t a coherent theme to assign a specific label, so Unknown best fits.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902307","count":1},{"id":"GO:0033028","count":1},{"id":"GO:1902647","count":1},{"id":"GO:0016477","count":1},{"id":"GO:0097212","count":1}]},{"hash":"274244535756566148","title":"Unknown","description":"The top GO terms are highly diverse (histone catabolic process, isotype switching, signal transduction regulation, ubiquitination, immune signaling, transcriptional regulation, dosage compensation) with no clear shared function, and there are no edges or interactions connecting the proteins. This suggests the cluster is not cohesively functionally related, so a meaningful label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0036205","count":1},{"id":"GO:0045190","count":1},{"id":"GO:0032487","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0039536","count":1}]},{"hash":"1000630741074634926","title":"Lipid metabolism and membrane trafficking","description":"The set of terms heavily points to lipid-related biology: positive regulation of the mevalonate pathway, lipid A biosynthesis, and sphingomyelin catabolic process, plus ER-to-Golgi vesicle-mediated transport indicating membrane trafficking. While there are some outliers related to vascular development and stress responses, the core themes center on lipid metabolism and membrane trafficking. ","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0001569","count":4},{"id":"GO:0016576","count":4},{"id":"GO:0035690","count":4},{"id":"GO:1900486","count":4},{"id":"GO:0006685","count":4}]},{"hash":"1773017128431474981","title":"Unknown","description":"The top GO terms span diverse areas\u2014endocrine signaling (insulin secretion, activin signaling), cardiac and neural development (ventricular morphogenesis, neuronal action potential), redox stress responses (response to hydrogen peroxide, redox state), and basic processes like cell division\u2014showing no single cohesive function for the cluster.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030073","count":3},{"id":"GO:0032925","count":3},{"id":"GO:1901710","count":3},{"id":"GO:0055010","count":3},{"id":"GO:0051775","count":3}]},{"hash":"511466666153148011","title":"Unknown","description":"The four proteins show two GO terms for ribosomal subunit biogenesis and two membrane/energy-related terms (proton motive force-driven ATP synthesis and monoatomic cation transmembrane transport). This mix suggests no single cohesive function tying all members together, making Unknown the most appropriate label.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042777","count":1},{"id":"GO:0099132","count":1},{"id":"GO:0042273","count":1},{"id":"GO:0042274","count":1}]},{"hash":"2037529842495507533","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0071441","count":2},{"id":"GO:0001178","count":2},{"id":"GO:0071035","count":2},{"id":"GO:0042766","count":2}]},{"hash":"843443967624789801","title":"Unknown","description":"The GO terms are heterogeneous, spanning mitochondrial dynamics, immune signaling, excretion, and dopaminergic synaptic activity, with no clear single function tying the proteins together. Therefore there is no coherent theme to name this cluster beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1903044","count":1},{"id":"GO:1903905","count":1},{"id":"GO:0001302","count":1},{"id":"GO:0070584","count":1},{"id":"GO:1990046","count":1}]},{"hash":"18491280179348103","title":"Developmental transcription regulators","description":"This cluster is characterized by GO terms centered on DNA-templated transcription and its regulation, plus development/morphogenesis terms (post-anal tail morphogenesis and bone morphogenesis). The common theme appears to be proteins involved in controlling gene expression during developmental morphogenesis. Confidence: Medium","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006355","count":1},{"id":"GO:0006351","count":1},{"id":"GO:0036342","count":1},{"id":"GO:0060349","count":1}]},{"hash":"389421656542216501","title":"Cardiovascular development and calcium signaling","description":"The cluster features heart development (GO:0007507) and branching in blood vessel morphogenesis (GO:0001569), with calcium-release regulation (GO:0051281) and long-term calcium signaling terms (GO:0060291, GO:1900271), supporting a cardiovascular development and calcium signaling theme. Noise from translation and neural synaptic terms exists but does not overshadow the core signals.","confidence":"Medium","size":4,"edges":4,"triangles":1,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071456","count":2},{"id":"GO:0002184","count":1},{"id":"GO:0006412","count":1},{"id":"GO:0001569","count":1},{"id":"GO:1901841","count":1}]},{"hash":"321661250203852266","title":"ER-Golgi Vesicle Trafficking and ER Retention","description":"These proteins share GO terms for ER-to-Golgi and Golgi-to-ER vesicle transport, ER lumen protein retention, and trafficking toward the plasma membrane, indicating a cohesive role in the secretory pathway and ER retention. The strongest signal is vesicle trafficking and ER retention.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090004","count":1},{"id":"GO:0006888","count":1},{"id":"GO:0071340","count":1},{"id":"GO:0006890","count":1},{"id":"GO:0006621","count":1}]},{"hash":"62309068446361627","title":"Unknown","description":"This cluster shows a mix of narrow GO terms (nucleotide salvage and pyrimidine metabolism) alongside diverse processes (plant-type cell wall organization, CoA biosynthesis, phosphorylation, detoxification), with little connectivity. There isn\u2019t a single, coherent function linking these proteins, so a meaningful, representative label cannot be assigned.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":1},{"id":"GO:0044211","count":1},{"id":"GO:0044206","count":1},{"id":"GO:0009405","count":1},{"id":"GO:0006238","count":1}]},{"hash":"1852644672621691220","title":"Oxidative Stress Response & Protein Repair","description":"The top GO terms center on redox-related processes and protein maintenance (e.g., cellular response to hydrogen peroxide, protein repair, protein modification), with additional references to oxidation-reduction and methionine salvage. Despite some unrelated terms likely representing annotation noise, the core signal points to mechanisms that cope with oxidative damage and preserve protein integrity.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0006464","count":1},{"id":"GO:1990355","count":1},{"id":"GO:0070301","count":1},{"id":"GO:0030091","count":1}]},{"hash":"163398469188351089","title":"mRNA Splicing and Processing","description":"This cluster is dominated by GO terms tied to splicing and spliceosome function (mRNA splicing via spliceosome, regulation of alternative splicing, splice-site recognition, small-subunit processome assembly) and mRNA modification, indicating proteins involved in RNA maturation and post-transcriptional regulation. While there are also terms related to translation initiation and ncRNA silencing, the core signal points to spliceosome-mediated mRNA processing.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0045292","count":3},{"id":"GO:0006378","count":3},{"id":"GO:0000381","count":2},{"id":"GO:0016556","count":2},{"id":"GO:0001825","count":2}]},{"hash":"749944216355448607","title":"Gene Expression and Cell Cycle Regulation","description":"The top GO terms point to regulation of gene expression (alternative splicing via spliceosome, transcriptional repression) and post-translational control (protein ubiquitination), plus processes tied to cell state (G0 to G1 transition) and broader developmental regulation (morphogenesis). The cluster appears to collect regulatory functions that modulate gene output and cellular progression, though the presence of diverse developmental terms introduces some breadth beyond a single pathway.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0000381","count":2},{"id":"GO:0016567","count":2},{"id":"GO:0071600","count":1},{"id":"GO:0045023","count":1},{"id":"GO:0000122","count":1}]},{"hash":"151707679862378507","title":"Unknown","description":"No GO terms or functional annotations are provided for this cluster (Top Terms is empty). Without functional evidence, there\u2019s no clear common theme linking these proteins, so a meaningful label cannot be assigned.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[]},{"hash":"2278060005511044856","title":"Unknown","description":"Top Terms are empty and there are no edges or interactions to suggest a common function, so a meaningful label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"1304746825490029226","title":"Unknown","description":"The listed GO terms encompass DNA replication/repair, stress granule disassembly, peroxisomal import, mitochondrial complex assembly, and proteasomal degradation, among others, with no single dominant function linking the proteins. This heterogeneity indicates there is no coherent theme to label; thus the cluster should be marked Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0035617","count":2},{"id":"GO:0000733","count":2},{"id":"GO:0051260","count":1},{"id":"GO:0016562","count":1}]},{"hash":"1261876988682049638","title":"Cell-Cell Adhesion and Cytoskeleton Regulation","description":"The top GO terms point to adhesion-related processes and actin cytoskeleton dynamics, including desmosome assembly, regulation of actin cytoskeleton by cell\u2013cell adhesion, and cell migration. These collectively suggest a theme around how cells adhere to neighbors and reorganize their cytoskeleton to move or maintain tissue structure, with some ancillary terms that are less central (e.g., vesicle assembly, brain development). Overall, the cluster most coherently maps to adhesion and cytoskeletal regulation.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:1904798","count":3},{"id":"GO:0086019","count":3},{"id":"GO:0071255","count":3},{"id":"GO:0032471","count":3},{"id":"GO:0016477","count":3}]},{"hash":"579499172474360786","title":"Microtubule dynamics and cytokinesis","description":"The top terms point strongly to microtubule-based processes: plus-end depolymerization, regulation of microtubule\u2013based processes, plus-end\u2013directed vesicle transport, and actomyosin contractile ring assembly during cytokinesis, as well as mitotic chromosome handling. Other terms (stress granule disassembly, growth regulation, chloroplast movement) may be ancillary or context-specific, but the central theme remains cytoskeletal dynamics and cell division.","confidence":"High","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0035617","count":2},{"id":"GO:0032487","count":1},{"id":"GO:0001560","count":1},{"id":"GO:0070462","count":1},{"id":"GO:0009904","count":1}]},{"hash":"347369018136224130","title":"Nuclear RNA processing and ribosome biogenesis","description":"The top GO terms point to RNA maturation and processing (SSU-rRNA maturation, tRNA processing, mRNA splicing, transcription termination, histone mRNA metabolism) with related nuclear import and mRNA handling (P-body assembly). Together, these indicate a cluster centered on RNA metabolism and ribosome biogenesis, with some peripheral terms (hair cycle, water deprivation) likely noise. Confidence: High.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042633","count":2},{"id":"GO:0051170","count":2},{"id":"GO:0030490","count":2},{"id":"GO:0008033","count":2},{"id":"GO:0008334","count":2}]},{"hash":"2059454357845383736","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:0006260","count":3},{"id":"GO:0071049","count":3},{"id":"GO:0071035","count":3},{"id":"GO:0034476","count":3},{"id":"GO:0071042","count":3}]},{"hash":"619472959694654722","title":"Translation Machinery and mRNA Decay","description":"The top GO terms are dominated by translation-related processes (translation, initiation, elongation, termination, and cytoplasmic translation) plus selenocysteine incorporation, and a deadenylation-dependent mRNA decay term, pointing to proteins involved in protein synthesis and associated mRNA turnover. A couple of less central terms (glial proliferation, cell division) are present but don\u2019t define the core function. Confidence in this label is High.","confidence":"","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006412","count":3},{"id":"GO:0000288","count":3},{"id":"GO:0051301","count":3},{"id":"GO:0006413","count":3},{"id":"GO:0006415","count":3}]},{"hash":"1880646143348052504","title":"Unknown","description":"The GO terms span neural and organ development (optic nerve morphogenesis, corpus callosum and lung mesenchyme development) as well as immune signaling and stress responses (B cell receptor signaling, cellular response to virus, apoptosis) plus migration and protein processing, with no single cohesive theme. This diversity makes it hard to assign a precise, unified function to the cluster.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016477","count":4},{"id":"GO:0010898","count":4},{"id":"GO:0060484","count":4},{"id":"GO:0022038","count":4},{"id":"GO:0050853","count":4}]},{"hash":"580910803506712144","title":"Unknown","description":"The GO terms are highly diverse, including positive regulation of apoptosis and peptidyl-threonine phosphorylation, cartilage condensation, visual perception, cell cycle and heart development, synaptic potentiation, and even plant-specific abscisic acid signaling. This broad mix across tissues, species, and processes provides no single unifying function for the cluster, so a concise label cannot be confidently assigned beyond Unknown.","confidence":"","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0043065","count":4},{"id":"GO:0010800","count":4},{"id":"GO:0001502","count":4},{"id":"GO:0007601","count":4},{"id":"GO:0000278","count":4}]},{"hash":"1490183404747761641","title":"Diverse membrane transporters","description":"This cluster shows strong GO enrichment for membrane transport across various compartments and substrates (xenobiotic export, daunorubicin and drug transport, taurine transport, peroxisomal fatty acid import, mitochondrial peptide export, teichoic acid transport), suggesting a shared function as transport proteins with a broad substrate range. A nucleotide-excision repair term is present but does not dominate, so the label remains representative of the cluster\u2019s primary theme.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046618","count":2},{"id":"GO:0006289","count":2},{"id":"GO:0015910","count":2},{"id":"GO:0015777","count":2},{"id":"GO:0043213","count":2}]},{"hash":"777133177278919370","title":"Embryonic morphogenesis and tissue development","description":"Dominant GO terms point to embryonic development and tissue morphogenesis across multiple tissues (cranial skeleton, corpus callosum, lung mesenchyme), with a couple of secondary terms related to proliferation and stress responses. This suggests the cluster primarily captures developmental morphogenesis rather than a single, specific pathway, though some terms are peripheral. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006260","count":2},{"id":"GO:0048701","count":2},{"id":"GO:0016477","count":1},{"id":"GO:0010898","count":1},{"id":"GO:0060484","count":1}]},{"hash":"1017890176817994646","title":"Developmental morphogenesis and tissue development","description":"The TOP GO terms are dominated by developmental and morphogenesis signals (optic nerve morphogenesis, corpus callosum development, lung-associated mesenchyme development, and cell migration), with supporting processes like protein processing and apoptotic regulation that often accompany development. While a few immune-related terms appear (B cell receptor signaling), the central pattern across the terms points to coordinated developmental/tissue morphogenesis rather than a single specialized function.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0016477","count":3},{"id":"GO:0010898","count":3},{"id":"GO:0060484","count":3},{"id":"GO:0022038","count":3},{"id":"GO:0050853","count":3}]},{"hash":"478545003545153204","title":"Unknown","description":"The GO terms span lipopolysaccharide biosynthesis, cobalamin biosynthesis, tRNA wobble uridine modification, metal transport (zinc, copper, cadmium), epoxygenase P450 pathway, response to testosterone, phospholipid dephosphorylation, and serine biosynthesis, which do not cohere into a single clear function for the cluster. There isn\u2019t a unifying biological theme strong enough to name the cluster confidently.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009103","count":3},{"id":"GO:0009236","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0071577","count":2},{"id":"GO:0006825","count":2}]},{"hash":"1416204634003802777","title":"Neural development and embryogenesis","description":"Based on the Top Terms, the strongest signal is developmental biology: neural tube closure, forebrain development, skeletal system development, and multicellular organism development, suggesting these proteins are involved in embryonic/neural development. A few other terms (defense response, ER stress\u2013related apoptosis, metal ion response) appear but do not cohesively define the same functional theme. Thus, the cluster is best described as related to neural development and embryogenesis, with some potential ancillary stress-related roles.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001843","count":3},{"id":"GO:0050830","count":3},{"id":"GO:0001403","count":3},{"id":"GO:0000278","count":3},{"id":"GO:0001501","count":3}]},{"hash":"1750443325235227648","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0046110","count":2},{"id":"GO:0021756","count":2},{"id":"GO:0032869","count":2},{"id":"GO:0032264","count":2},{"id":"GO:0044209","count":2}]},{"hash":"1994615922515060789","title":"Proteoglycan Biosynthesis and ECM Signaling","description":"The GO terms are dominated by proteoglycan biosynthesis (chondroitin sulfate, heparan/heparin proteoglycans) and related glycosylation, plus ECM-related signaling (BMP signaling, ossification), suggesting a cluster focused on extracellular matrix production and its developmental signaling roles.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0050650","count":1},{"id":"GO:0006044","count":1},{"id":"GO:0045743","count":1},{"id":"GO:0006486","count":1},{"id":"GO:0007492","count":1}]},{"hash":"403361164041635641","title":"Neural Development and Amino Acid Metabolism","description":"This cluster links neural development terms (forebrain development, neuromuscular control) with amino-acid\u2013related metabolic catabolic processes (GABA, putrescine, glycine betaine, formyl-THF), suggesting a cohesive group involved in neural maturation alongside amino-acid metabolism.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0009450","count":4},{"id":"GO:0009447","count":4},{"id":"GO:0019285","count":4},{"id":"GO:0009258","count":4},{"id":"GO:0048738","count":4}]},{"hash":"225817248539611395","title":"Ion transport and pH regulation","description":"The top GO terms are dominated by membrane transport and pH regulation: proton transmembrane transport, sodium ion export across plasma membrane, and vacuolar acidification. This suggests a common theme around maintaining ion gradients and vesicular pH, though a few terms (metabolic catabolism, signaling pathways, and cardiac conduction) seem less related, possibly reflecting annotation noise or secondary roles.","confidence":"Medium","size":4,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0007035","count":1},{"id":"GO:0051595","count":1},{"id":"GO:0009097","count":1},{"id":"GO:0071268","count":1},{"id":"GO:0046392","count":1}]},{"hash":"216922828339384807","title":"Unknown","description":"The terms cover antibiotic response, hormone metabolism (androgen/glucocorticoid), transcription regulation, development, and various biosynthetic/catabolic processes with no clear common function or interaction pattern among the proteins (no edges). This lack of a cohesive theme suggests no specific cluster label.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046677","count":2},{"id":"GO:0008209","count":1},{"id":"GO:0006355","count":1},{"id":"GO:0006710","count":1},{"id":"GO:0030324","count":1}]},{"hash":"75429646345010345","title":"Amino acid catabolism and central carbon metabolism","description":"The cluster\u2019s GO terms cluster around amino acid degradation and related central carbon pathways (glycine, alanine, serine, cysteine), pyruvate biosynthesis, and glyoxylate cycling, indicating a metabolic focus on amino acid-derived carbon flow. The presence of [2Fe-2S] cluster assembly hints at cofactors necessary for metabolic enzymes, while sporadic terms like response to glucocorticoid and cAMP are less central. Overall, the dominant theme is amino acid catabolism feeding into central carbon metabolism.","confidence":"Medium","size":4,"edges":6,"triangles":4,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0042866","count":2},{"id":"GO:0044571","count":2},{"id":"GO:0051384","count":2},{"id":"GO:0019448","count":2},{"id":"GO:0046724","count":2}]},{"hash":"91280602124241439","title":"Membrane Transport of Substrates","description":"The proteins in this cluster are linked to diverse transmembrane transport processes, including xenobiotic export, drug (daunorubicin) transport, taurine and fatty acid import into organelles, teichoic acid transport, bacteriocin handling, and oligopeptide export from mitochondria, suggesting a shared theme of transporting various substrates across membranes. An outlier GO term for nucleotide-excision repair exists, but the dominant pattern is substrate transport, supporting this label.","confidence":"Medium","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0046618","count":1},{"id":"GO:0006289","count":1},{"id":"GO:0015910","count":1},{"id":"GO:0015777","count":1},{"id":"GO:0043213","count":1}]},{"hash":"700597825255407643","title":"Unknown","description":"Top terms are disparate: neurotransmitter transport (neuronal function), protein homooligomerization, protein ubiquitination, and an obsolete regulation of DNA topoisomerase activity. Only single annotations per term, no shared pathway or process. Without a coherent theme, a meaningful label cannot be assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006836","count":1},{"id":"GO:0051260","count":1},{"id":"GO:2000372","count":1},{"id":"GO:0016567","count":1}]},{"hash":"523106849908556804","title":"Neuronal development and synaptic organization","description":"The top GO terms point to neuronal development (substantia nigra development) and dendritic spine morphogenesis, supporting a neuronal and synaptic context. Additional terms on adherens junctions, cell polarity, and regulated secretory pathways suggest broader cellular organization and trafficking, with mitochondrial-ER tethering signaling organelle interactions common in neurons. Overall, the cluster appears to group proteins involved in neuronal development, spine formation, and related cellular organization.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0021762","count":4},{"id":"GO:0008283","count":4},{"id":"GO:0061001","count":3},{"id":"GO:1990456","count":3},{"id":"GO:1902542","count":3}]},{"hash":"1416213845950998262","title":"Histone demethylases and protein hydroxylases","description":"This cluster features GO terms for histone demethylation (H3K4 and H3K36) and multiple peptidyl hydroxylation activities, pointing to enzymes that modify chromatin and other proteins post-translationally. The inclusion of regulatory terms like Notch signaling and osteoblast differentiation suggests these proteins act as broad epigenetic and PTM regulators with developmental roles. Given the emphasis on histone demethylation plus various hydroxylation activities, labeling as histone demethylases and protein hydroxylases captures the common function of the cluster.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0034720","count":2},{"id":"GO:0070544","count":2},{"id":"GO:0045668","count":2},{"id":"GO:0030961","count":2},{"id":"GO:2001214","count":1}]},{"hash":"1656006457793815880","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":3,"triangles":0,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0071031","count":3},{"id":"GO:0000398","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0071035","count":2},{"id":"GO:0006306","count":2}]},{"hash":"213407708662615699","title":"Unknown","description":"The top terms are a mix of RNA processing, gene silencing, ubiquitination, signaling regulation, and various development/morphogenesis terms, with no clear shared function or interaction among the proteins (no edges). This makes it impossible to assign a cohesive, representative label.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006397","count":2},{"id":"GO:0045433","count":1},{"id":"GO:0051865","count":1},{"id":"GO:0021610","count":1},{"id":"GO:0021965","count":1}]},{"hash":"1465420409936417303","title":"Ribosome Biogenesis and Secretory Trafficking","description":"This cluster centers on ribosome biogenesis and ribosomal export, and includes terms for Golgi-to-plasma membrane transport, apical protein localization, and ER stress response, pointing to a common theme of protein synthesis and intracellular trafficking. While neural development terms appear, the strongest signals relate to ribosome assembly/export and the secretory pathway, supporting a cohesive label.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:1902307","count":1},{"id":"GO:0033028","count":1},{"id":"GO:0043001","count":1},{"id":"GO:0042461","count":1}]},{"hash":"2194793009610990717","title":"Sec-dependent protein transport","description":"The cluster is dominated by GO terms tied to Sec-mediated protein movement and targeting across membranes, including Sec transport, protein import, intracellular transmembrane transport, and general protein targeting, indicating a shared role in secretory/transport functions. The single ROS-related term is contextual rather than central to the core function. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0052059","count":1},{"id":"GO:0006605","count":1},{"id":"GO:0043952","count":1},{"id":"GO:0017038","count":1},{"id":"GO:0065002","count":1}]},{"hash":"38255429265125722","title":"Nuclear chromosome condensation and segregation","description":"The dominant GO terms point to chromosome architecture and dynamics during the cell cycle, including mitotic chromosome condensation, sister chromatid cohesion, nuclear chromosome segregation, and related DNA replication activity. There are a couple of outliers (antibiotic biosynthetic process and tRNA wobble uridine modification) that seem less connected to chromosomal functions, so the core theme remains chromosome condensation/segregation. ","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0017000","count":2},{"id":"GO:0002098","count":2},{"id":"GO:0010032","count":1},{"id":"GO:0098813","count":1},{"id":"GO:0007064","count":1}]},{"hash":"1285219475223213525","title":"Heat stress and ER protein quality control","description":"This cluster is driven by GO terms related to heat response, protein folding in the endoplasmic reticulum, response to unfolded proteins, and nuclear protein quality control via the ubiquitin-proteasome system. Together these indicate a cohesive theme of managing protein folding and stability under stress (heat/ER stress), with quality control mechanisms. Some other terms present (DNA replication, specific signaling pathway regulation) seem incidental to this core function.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":1},{"id":"GO:0006260","count":1},{"id":"GO:1900035","count":1},{"id":"GO:1901621","count":1},{"id":"GO:0034975","count":1}]},{"hash":"821541388114826591","title":"Calcium Signaling in Heart and Synapses","description":"The terms point to calcium-dependent processes: long-term potentiation and regulation of cytosolic calcium release, coupled with heart development and vascular branching. While a few items are broader (xenobiotic response, transcription regulation) the central theme appears to be calcium-mediated signaling in both neural and cardiovascular contexts, justifying this label.","confidence":"Medium","size":4,"edges":5,"triangles":2,"max_degree":3,"top_function":null,"top_go_terms":[{"id":"GO:0097274","count":2},{"id":"GO:0001569","count":1},{"id":"GO:1901841","count":1},{"id":"GO:1900271","count":1},{"id":"GO:0060291","count":1}]},{"hash":"2025807873037736690","title":"Mitochondrial transport and membrane potential regulation","description":"The top GO terms cluster around mitochondrial membrane properties and metabolite transport: ADP/ATP transport, alpha-ketoglutarate transport, magnesium export, and regulation of membrane permeability and potential. Some terms relate to insulin/IGF signaling, but the dominant theme is mitochondrial metabolite transport and energy maintenance.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046902","count":3},{"id":"GO:0051881","count":3},{"id":"GO:0015742","count":3},{"id":"GO:0032869","count":3},{"id":"GO:1990314","count":3}]},{"hash":"2165845880023273664","title":"Unknown","description":"The terms across the four proteins span proteolysis, biosynthetic and metabolic processes (phytochelatin and cholesterol biosynthesis), autophagy regulation, protein complex formation, receptor trafficking, and neural signaling-related processes, with no clear single function or pathway tying them together. With zero edges and no cohesive theme, there isn\u2019t a reliable label beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006508","count":2},{"id":"GO:0046938","count":1},{"id":"GO:1904715","count":1},{"id":"GO:0043085","count":1},{"id":"GO:0006695","count":1}]},{"hash":"2072778763669871333","title":"Muscle actin organization and myofibril assembly","description":"Top GO terms point to regulation of the actin cytoskeleton, cardiac myofibril assembly, actin filament organization, and actomyosin contractile ring formation, with additional but weaker signals for muscle differentiation and cell shape changes. This pattern suggests a cohesive theme of actin-based muscle structure development and assembly of contractile apparatus, rather than general cytoskeletal remodeling. Confidence in this label is High.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0008360","count":2},{"id":"GO:0055003","count":2},{"id":"GO:2001015","count":2},{"id":"GO:1904670","count":1},{"id":"GO:0051758","count":1}]},{"hash":"2152476429199095065","title":"Unknown","description":"The GO terms are heterogeneous, including antiviral responses (interferon-alpha, exogenous dsRNA) alongside GPCR signaling and morphine response, with several obsolete terms and no observed edges linking the proteins. This lacks a clear, cohesive functional theme, so a specific, representative name cannot be confidently assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0006478","count":3},{"id":"GO:0051348","count":3},{"id":"GO:0016576","count":3},{"id":"GO:1903071","count":3},{"id":"GO:0035457","count":3}]},{"hash":"1570901782754426550","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning DNA recombination, renal water transport, aging (obsolete), corneocyte development, cell-cycle regulation, phosphatidylinositol dephosphorylation, xenobiotic response, and glycogen regulation. With no clear shared function or process and no edges in the cluster, there isn\u2019t a coherent theme to name a specific function.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006310","count":2},{"id":"GO:2001153","count":1},{"id":"GO:0007568","count":1},{"id":"GO:0080111","count":1},{"id":"GO:1900087","count":1}]},{"hash":"2198839186878145941","title":"Unknown","description":"The top GO terms cover mitochondrial ribosome and respiratory chain complex III assembly, peroxisomal matrix import, protein oligomerization, and DNA replication-related processes, spanning multiple organelles and functions with no single cohesive theme. I cannot identify a unique, representative function for this cluster.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0006067","count":1},{"id":"GO:0061668","count":1},{"id":"GO:0051260","count":1},{"id":"GO:0016562","count":1},{"id":"GO:0006260","count":1}]},{"hash":"2110485474702837415","title":"Golgi UDP-sugar transporters","description":"These proteins appear to function as nucleotide-sugar transporters in the Golgi, given GO terms for transmembrane transport of UDP-galactose and UDP-GlcNAc into the Golgi lumen and related glycosylation processes. The presence of plant-specific terms like pollen exine formation and shoot apical meristem regulation suggests a role in Golgi-dependent glycan biosynthesis that supports pollen wall development and meristem activity. Together, these indicate a coherent niche as Golgi-localized nucleotide-sugar transporters in plants.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0097624","count":1},{"id":"GO:1990569","count":1},{"id":"GO:1903857","count":1},{"id":"GO:0010584","count":1},{"id":"GO:1902183","count":1}]},{"hash":"1943240215811032530","title":"Nematode molting and pharyngeal pumping","description":"These terms point to nematode-specific biology: a molting cycle involving cuticle remodeling and the pharyngeal pumping mechanism used for feeding. Taken together, they suggest a cluster of proteins involved in nematode development and physiology, though the two functions are somewhat disparate, and the small, edge-free cluster makes the connection tentative. ","confidence":"Low","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018996","count":1},{"id":"GO:0043050","count":1}]},{"hash":"2749734519484766","title":"Diverse Substrate Membrane Transport","description":"This cluster is characterized by GO terms for various substrate transmembrane transport (nitrate, arabinose, urate, glucose import, trehalose, nitrite, sodium ions, etc.), indicating a general membrane transport function. An outlier term on replicative senescence is likely noise, but the dominant theme ties to transporter activity across membranes.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015706","count":1},{"id":"GO:1904728","count":1},{"id":"GO:0015751","count":1},{"id":"GO:0044381","count":1},{"id":"GO:0015747","count":1}]},{"hash":"50463884972170466","title":"Diverse Metabolic Pathways","description":"This cluster\u2019s top GO terms span a wide range of biosynthetic and catabolic processes (cobalamin biosynthesis, lignin biosynthesis, catecholamine metabolism, fatty acid biosynthesis, amino acid activation for nonribosomal peptide biosynthesis, etc.), with no clear single function tying all proteins together. The diversity suggests a general metabolic/metabolic-assembly theme rather than one cohesive pathway.","confidence":"Low","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009236","count":1},{"id":"GO:0042135","count":1},{"id":"GO:0009809","count":1},{"id":"GO:0006584","count":1},{"id":"GO:0006479","count":1}]},{"hash":"1196933949088612704","title":"Unknown","description":"GO terms are spread across neural signaling (synaptic plasticity, dopamine response), heart development and hypertrophy, cholesterol biosynthesis, and cell-cycle regulation (mitotic checkpoint, chromatid cohesion). With only one edge and no coherent shared process, there is no clear functional theme tying these proteins together.","confidence":"","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046330","count":2},{"id":"GO:0006695","count":1},{"id":"GO:0007095","count":1},{"id":"GO:0010614","count":1},{"id":"GO:0060291","count":1}]},{"hash":"1015473544269898093","title":"Membrane Ion and Metabolite Transport","description":"The GO terms cluster around transmembrane transport of ions (sodium, potassium, arsenite) and various metabolites (succinate, citrate, malate), plus general transmembrane transport, indicating a transport module across membranes; the skeletal morphogenesis term is likely noise and not central to the cluster\u2019s function.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015700","count":2},{"id":"GO:2000185","count":2},{"id":"GO:0006814","count":2},{"id":"GO:0055085","count":2},{"id":"GO:0006813","count":2}]},{"hash":"249074883573717380","title":"Ubiquitin-Mediated Proteostasis and Stress Signaling","description":"This cluster centers on ubiquitination processes (K63-linked ubiquitination, autoubiquitination) and chaperone-mediated protein assembly, pointing to roles in protein quality control; it also includes responses to various stresses and hormones (ethanol, chitin, glucocorticoid metabolism), suggesting broader ubiquitin-dependent stress signaling. The combination of proteostasis-related functions and stress responses supports a label focused on ubiquitin-regulated proteostasis and signaling rather than a single, narrow pathway.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090035","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0051865","count":3},{"id":"GO:0071361","count":3},{"id":"GO:0030579","count":3}]},{"hash":"292118781630912759","title":"Unknown","description":"Top terms show a mix of metabolic processes (thiamine, tetrahydrofolate, proline catabolism) and broad differentiation/proliferation programs (erythrocyte, neuron, stem cell proliferation), with no single cohesive function linking the proteins. This makes it hard to assign a specific, representative label beyond Unknown.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046886","count":4},{"id":"GO:0009228","count":4},{"id":"GO:0045648","count":4},{"id":"GO:0046653","count":4},{"id":"GO:2000648","count":4}]},{"hash":"2177258295924517497","title":"Germline Stem Cell Development and Genome Maintenance","description":"The cluster centers on germline biology, with GO terms for both male germ-line cyst encapsulation and female germ-line stem cell population maintenance, plus stem cell differentiation. It also includes DNA damage recognition and proteostasis processes (proteasome assembly and positive regulation of proteasomal ubiquitin-dependent protein catabolic process), implying a theme of genome and protein quality control that supports germline stem cell development and maintenance.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0048140","count":1},{"id":"GO:0090054","count":1},{"id":"GO:0000715","count":1},{"id":"GO:0036099","count":1},{"id":"GO:0043248","count":1}]},{"hash":"1928276703228301949","title":"Unfolded Protein Response and Kinase Regulation","description":"The top GO terms point to an ER stress/UPR theme (response to unfolded protein) and modulation of signaling kinases (negative regulation of protein kinase activity), with a secondary cue toward ubiquitin-related protein quality control. While some terms are obsolete or noisy, the core signals suggest a cluster involved in managing misfolded proteins and adjusting kinase signaling.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006986","count":2},{"id":"GO:0006469","count":2},{"id":"GO:0051348","count":1},{"id":"GO:0016576","count":1},{"id":"GO:1903071","count":1}]},{"hash":"887843862556161033","title":"Unknown","description":"The top GO terms cover a highly diverse set of processes\u2014from behavior (locomotory/psychomotor, fear) to stress responses (hypoxia, oxidant detoxification) and various cellular processes (cell adhesion, endothelial migration, proteolysis, symbiont entry, insulin secretion regulation). This lack of a single cohesive function makes it hard to assign a specific, representative label. Confidence: None","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0035641","count":2},{"id":"GO:0036343","count":2},{"id":"GO:0001666","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0007155","count":2}]},{"hash":"1919990071840493852","title":"Synaptic plasticity and brain development","description":"This cluster shows strongest enrichment for neuronal functions, notably brain development and long-term potentiation with regulation of synaptic plasticity, pointing to roles in synaptic signaling and development. The presence of a few housekeeping terms (ribophagy, nuclear mRNA/tRNA export) likely reflects broader cellular roles of shared proteins, but the dominant theme remains synaptic regulation.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007420","count":2},{"id":"GO:0051260","count":2},{"id":"GO:0034517","count":1},{"id":"GO:0060291","count":1},{"id":"GO:0031914","count":1}]},{"hash":"1538215984109739601","title":"Plant light sensing and photosynthesis","description":"Most top GO terms describe responses to different light conditions (high/low light, red/blue/UV-A) and core photosynthetic processes (photosynthesis, photosystem II light harvesting, nonphotochemical quenching) as well as chlorophyll/chromophore components (phytol biosynthesis). This coherent set suggests a functional cluster centered on light perception and photosynthetic machinery in plants.","confidence":"High","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071486","count":1},{"id":"GO:0009645","count":1},{"id":"GO:0018298","count":1},{"id":"GO:1904964","count":1},{"id":"GO:0010114","count":1}]},{"hash":"1579216751966420287","title":"Acetylation-Related Protein Modification","description":"The GO terms are dominated by acetylation-related processes (N-terminal acetylation, peptidyl-lysine acetylation, histone acetylation, and various acetylation modifiers like propionylation and spermine acetylation), indicating a shared function in acetyl group transfer/modification of proteins and amines; a few terms (leaf formation, ectoine biosynthesis) seem ancillary noise, but the central theme is acetylation chemistry.","confidence":"Medium","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009447","count":3},{"id":"GO:0018003","count":3},{"id":"GO:2000025","count":3},{"id":"GO:0006044","count":3},{"id":"GO:0032919","count":3}]},{"hash":"461228539564276708","title":"Mitochondrial and Vacuolar Membrane Transport","description":"The terms cluster around transport across organelle membranes (mitochondria and vacuoles) and related maintenance processes, including proton translocation, mitochondrial complex IV assembly, xenobiotic transport, vacuolar transport/fusion, and microautophagy, suggesting a membrane-transport/or organelle-maintenance role for the proteins. The small size of the cluster and modest interconnectivity keep the label plausible but not definitive.","confidence":"Medium","size":4,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042774","count":1},{"id":"GO:0033617","count":1},{"id":"GO:1902600","count":1},{"id":"GO:0006855","count":1},{"id":"GO:0006799","count":1}]},{"hash":"735537098478458455","title":"Unknown","description":"The four proteins show a scattered set of GO terms across lipid metabolism (sphingomyelin catabolic process, lipid A biosynthetic process, mevalonate pathway), vesicle transport (ER to Golgi transport), and vascular or stress-related processes (branching in blood vessel morphogenesis, cardiac hypertrophy), with many obsoletes present and no evident functional connection or interaction among the proteins. There is no cohesive theme tying the terms together, so a specific functional label cannot be confidently assigned.","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001569","count":1},{"id":"GO:0016576","count":1},{"id":"GO:0035690","count":1},{"id":"GO:1900486","count":1},{"id":"GO:0006685","count":1}]},{"hash":"1618882380593871237","title":"Unknown","description":"Unknown","confidence":"","size":4,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009443","count":1},{"id":"GO:0014067","count":1},{"id":"GO:0060665","count":1},{"id":"GO:1904937","count":1},{"id":"GO:0046716","count":1}]},{"hash":"391505769728874068","title":"Oxidative Stress Response","description":"This small cluster is dominated by terms tied to oxidative stress and redox biology: response to hydrogen peroxide and response to redox state, plus an obsolete term about transcriptional regulation in response to oxidative stress. A few single-term entries (insulin secretion, heart morphogenesis, neuronal signaling) appear weakly, suggesting the core theme is redox-responsive stress signaling rather than a single cohesive pathway. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0036091","count":2},{"id":"GO:0030073","count":1},{"id":"GO:0032925","count":1},{"id":"GO:1901710","count":1},{"id":"GO:0055010","count":1}]},{"hash":"1708976039315966087","title":"Neuronal signaling and synapse organization","description":"The top GO terms cluster around neural signaling and synaptic processes (ERK cascade regulation, synapse organization, neuronal apoptotic regulation) and modulation of major pathways (Wnt, TGF-beta). This suggests a group of proteins that modulate neuronal signaling and synaptic structure, with some related roles in proteostasis.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0070373","count":2},{"id":"GO:0050821","count":1},{"id":"GO:0050808","count":1},{"id":"GO:0061051","count":1},{"id":"GO:0090263","count":1}]},{"hash":"2189528466969813073","title":"Ubiquitin-Proteasome Regulation","description":"The three proteins appear linked by terms centered on ubiquitination and proteasomal degradation (SCF-dependent ubiquitin-protein catabolic process; protein deubiquitination) and by signaling pathways commonly modulated by ubiquitination, such as NF-kappaB and canonical Wnt signaling. Additional terms touching inflammatory and antiviral responses fit downstream effects of ubiquitin-regulated signaling. This suggests a common theme around proteostasis and signaling regulation via the ubiquitin-proteasome system, despite the presence of some broad/obsolete GO terms. Confidence: Medium","confidence":"","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":1},{"id":"GO:0019878","count":1},{"id":"GO:0031146","count":1},{"id":"GO:0038061","count":1},{"id":"GO:0010043","count":1}]},{"hash":"2002768564317382365","title":"Unknown","description":"The top GO terms are scattered across distinct biological processes (visual perception, proteolysis, ribosomal RNA maturation, translation) with no clear common function linking the proteins. The cluster has no reported edges or interactions, suggesting possible noise or unrelated proteins merged in the cluster, so a specific functional label does not emerge.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007601","count":1},{"id":"GO:0006508","count":1},{"id":"GO:0000462","count":1},{"id":"GO:0006412","count":1}]},{"hash":"435017218953250116","title":"Nuclear transcription and RNA processing regulation","description":"This cluster centers on regulation of gene expression at the nuclear level, with GO terms for transcription by RNA polymerase II, regulation of mRNA and tRNA export from the nucleus, and chromatin/modification processes (histone methylation, monoubiquitination). Although a few terms (ribophagy, synapse organization) are less directly connected, the dominant theme is nuclear control of transcription and RNA processing.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0045944","count":3},{"id":"GO:0034517","count":2},{"id":"GO:0050808","count":2},{"id":"GO:0032443","count":2},{"id":"GO:2000238","count":2}]},{"hash":"236822161479973159","title":"Ubiquitin-mediated proteostasis","description":"The top GO terms are dominated by ubiquitination and proteostasis-related processes (K63-linked ubiquitination, autoubiquitination, ERAD-related terms) and chaperone-mediated protein complex assembly, pointing to a cluster centered on the ubiquitin-proteasome system and protein quality control. Additional stress- and hormone-related responses (ethanol, chitin, glucocorticoid metabolism) are present but secondary, suggesting the core function is ubiquitin-dependent regulation and protein turnover. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0090035","count":2},{"id":"GO:0070534","count":2},{"id":"GO:0051865","count":2},{"id":"GO:0071361","count":2},{"id":"GO:0030579","count":2}]},{"hash":"2249208633094394766","title":"Protein Folding and ER Stress Response","description":"The cluster\u2019s top GO terms center on unfolded protein handling, chaperone-assisted refolding, and ER stress response, suggesting a core function in protein quality control and folding within the endoplasmic reticulum. Some unrelated terms (iron-sulfur cluster assembly, DNA replication, fungal-specific processes) appear as noise but do not outweigh the dominant folding/ER stress theme.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0070389","count":3},{"id":"GO:0016226","count":3},{"id":"GO:0070880","count":3},{"id":"GO:1903382","count":3},{"id":"GO:1902037","count":3}]},{"hash":"1651164122004388629","title":"Ubiquitin-Dependent Protein Degradation","description":"This cluster is dominated by GO terms related to ubiquitination and subsequent protein degradation (autoubiquitination, ubiquitin-dependent ERAD, polyubiquitination, protein catabolic process) with additional links to degradation of signaling components (Wnt receptor catabolic process) and growth/cell-cycle regulation, pointing to a cohesive role in ubiquitin\u2011mediated turnover of proteins.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":3},{"id":"GO:0030433","count":3},{"id":"GO:0071157","count":2},{"id":"GO:0042787","count":2},{"id":"GO:0046621","count":2}]},{"hash":"2041636308664959938","title":"Heterochromatin Formation and Telomere Maintenance","description":"The GO terms point to chromatin silencing and heterochromatin maintenance (e.g., silent mating-type cassette heterochromatin formation; DNA methylation-dependent constitutive heterochromatin formation; heterochromatin maintenance) with a notable emphasis on telomere regulation (regulation of telomere maintenance, nucleolar rDNA repeats localization). While a few terms touch on mitophagy and protein quality control, the dominant signal is chromatin organization and genome stability, especially around heterochromatin and telomeres.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030466","count":3},{"id":"GO:0061734","count":3},{"id":"GO:0070845","count":3},{"id":"GO:0006346","count":3},{"id":"GO:0034503","count":3}]},{"hash":"1776634554188729718","title":"Unknown","description":"The top GO terms span diverse processes (cardiac cell communication, brown fat differentiation, cell migration, NF-kappaB regulation, protein localization, inflammatory chemokine production, pain perception, and hepatocyte apoptosis) with no clear shared function. With 0 edges among the proteins, there isn\u2019t a cohesive biological theme to tie the proteins together, so a specific functional label isn\u2019t justifiable.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0086070","count":1},{"id":"GO:1903444","count":1},{"id":"GO:0016477","count":1},{"id":"GO:0007253","count":1},{"id":"GO:0072660","count":1}]},{"hash":"806082588555830314","title":"Heterochromatin maintenance and telomere regulation","description":"These proteins are predominantly involved in chromatin silencing and heterochromatin maintenance, including DNA methylation-dependent heterochromatin formation and silencing at mating-type loci, as well as telomere regulation and nucleolar rDNA localization. Although a few terms point to mitochondrial quality control and misfolded protein transport, the strongest signal is nuclear chromatin organization and genome stability, justifying this label.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA-templated transcription","top_go_terms":[{"id":"GO:0030466","count":3},{"id":"GO:0061734","count":3},{"id":"GO:0070845","count":3},{"id":"GO:0006346","count":3},{"id":"GO:0034503","count":3}]},{"hash":"879914542020783643","title":"Actin cytoskeleton remodeling and organization","description":"The terms cluster around actin dynamics: Arp2/3-mediated actin nucleation, sarcomere and postsynaptic actin organization, platelet aggregation, and roles in mitotic cytokinesis and chromosome movement, indicating a shared function in actin filament assembly and structural organization across cell processes.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070527","count":3},{"id":"GO:0016344","count":3},{"id":"GO:0042766","count":3},{"id":"GO:0000281","count":3},{"id":"GO:0034314","count":3}]},{"hash":"452488854154682288","title":"Neuronal Hypoxia-Driven Stress and Apoptosis","description":"The most represented terms are neuron apoptotic process, cellular response to hypoxia, and glycolytic process, pointing to a neuronal stress response with metabolic adaptation under hypoxic conditions. While other terms touch on signaling and development, the core pattern centers on neuronal stress signaling and energy metabolism under oxygen limitation, which justifies this label.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051402","count":2},{"id":"GO:0071456","count":2},{"id":"GO:0006096","count":2},{"id":"GO:0048705","count":1},{"id":"GO:0031146","count":1}]},{"hash":"713182376825224845","title":"Ubiquitination-regulated protein turnover","description":"The cluster is enriched for ubiquitination-related terms (autoubiquitination, K63-linked ubiquitination, ubiquitin-dependent processes) and degradation-related pathways (ribophagy), along with broad regulatory terms. This points to proteins involved in ubiquitin signaling that modulate turnover and regulation across pathways, justifying the label.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051865","count":3},{"id":"GO:0030579","count":3},{"id":"GO:0070534","count":3},{"id":"GO:0043547","count":3},{"id":"GO:0034517","count":2}]},{"hash":"863800970069537433","title":"Nuclear transport and transcription regulation under ER stress","description":"This cluster centers on processes regulating nuclear transport and transcription (e.g., negative regulation of protein export from the nucleus, transcription by RNA polymerase II, and DNA binding), with an additional ER stress response signal. The mix suggests a nuclear regulatory module coordinating transcriptional control under cellular stress, rather than a single isolated pathway.","confidence":"Medium","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0046826","count":2},{"id":"GO:0006351","count":2},{"id":"GO:0098869","count":2},{"id":"GO:0033158","count":1},{"id":"GO:0034976","count":1}]},{"hash":"1920404418491668195","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"regulatory ncRNA-mediated gene silencing","top_go_terms":[{"id":"GO:0031047","count":3},{"id":"GO:0048026","count":3},{"id":"GO:0071441","count":2},{"id":"GO:0001178","count":2},{"id":"GO:0071894","count":2}]},{"hash":"1324828867336975760","title":"Heat-shock response and chaperone activity","description":"Based on the top GO terms, these proteins cluster around heat-induced protein folding and stabilization (GO:0009408, GO:0050821, GO:0051086, GO:0051085). The presence of obsolete chaperone terms supports a folding/chaperone theme, while virion assembly and TNF-related terms seem peripheral. Thus the cluster best fits a heat-shock/chaperone activity theme.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0050821","count":3},{"id":"GO:0019068","count":3},{"id":"GO:0051086","count":3},{"id":"GO:0033198","count":3}]},{"hash":"1215696250677856748","title":"Vascular development and synaptic plasticity","description":"This cluster shows enrichment for heart development and blood vessel morphogenesis, paired with long-term synaptic potentiation and calcium/cGMP signaling terms, suggesting shared roles in cardiovascular development and neural signaling pathways (e.g., NO-cGMP and calcium dynamics).","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0001569","count":3},{"id":"GO:1901841","count":3},{"id":"GO:1900271","count":3},{"id":"GO:0060291","count":3},{"id":"GO:0090151","count":3}]},{"hash":"1693880367185104473","title":"Steroid Hormone Biosynthesis and Metabolism","description":"The GO terms are dominated by steroid-related processes (C21-steroid hormone biosynthetic, androgen, and progesterone metabolic processes), indicating a cohesive theme of steroid hormone biosynthesis and metabolism. Additional lipid metabolism terms (bile acid biosynthesis) and related signaling (prostaglandin response) are present as supporting context, but the core signal is steroid hormone production and turnover.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0071799","count":1},{"id":"GO:0001894","count":1},{"id":"GO:0006699","count":1},{"id":"GO:0018931","count":1}]},{"hash":"2056302958471533001","title":"Actin Cytoskeleton Organization and Dynamics","description":"This cluster centers on actin cytoskeleton remodeling: Arp2/3-mediated actin nucleation, sarcomere and postsynaptic actin organization, and mitotic cytokinesis, with platelet aggregation also linked to actin dynamics; a couple terms are obsolete or less directly related, but the core theme is actin-driven structural changes.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0070527","count":1},{"id":"GO:0016344","count":1},{"id":"GO:0042766","count":1},{"id":"GO:0000281","count":1},{"id":"GO:0034314","count":1}]},{"hash":"2076228551043061696","title":"DNA replication and repair proteins","description":"The top GO terms are dominated by DNA replication, replication checkpoint signaling, UV-damage excision repair, and translesion synthesis, all pointing to genome maintenance and DNA damage response. A few unrelated terms appear (peroxisome import, mitochondrial complex III assembly), but the core theme centers on DNA replication and repair functions.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":1},{"id":"GO:0016562","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0034214","count":1},{"id":"GO:0034551","count":1}]},{"hash":"2069204156988671562","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":"mitotic cell cycle","top_go_terms":[{"id":"GO:0060271","count":3},{"id":"GO:0050709","count":3},{"id":"GO:0006547","count":3},{"id":"GO:0007117","count":3},{"id":"GO:0051301","count":3}]},{"hash":"1326992240565268321","title":"Unknown","description":"There are no shared GO terms or interactions to tie these proteins to a common function, and the cluster has no edges or detectable enrichment, so a cohesive theme cannot be inferred.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[]},{"hash":"171954968111465492","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009048","count":2},{"id":"GO:0036205","count":1},{"id":"GO:0048536","count":1},{"id":"GO:0061158","count":1},{"id":"GO:0097039","count":1}]},{"hash":"176076438316727876","title":"Calcium-Dependent Signaling in Heart and Brain","description":"The top GO terms center on calcium ion release regulation and calcium signaling (e.g., positive regulation of release of sequestered calcium into cytosol) together with heart development and branching in blood vessels, as well as long-term synaptic potentiation. This suggests a shared role for Ca2+-mediated signaling influencing both cardiovascular development and neural synaptic plasticity, even though the cluster is small and the terms are diverse. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001569","count":1},{"id":"GO:1901841","count":1},{"id":"GO:1900271","count":1},{"id":"GO:0060291","count":1},{"id":"GO:0090151","count":1}]},{"hash":"190246105328190354","title":"ER Folding and Proteostasis Under Heat Stress","description":"Top terms cluster around ER protein folding, unfolded protein response, and ubiquitin-proteasome\u2013mediated quality control, pointing to a proteostasis function under heat stress. While a few terms (like DNA replication and translational frameshifting) reflect general cellular processes, the dominant theme is chaperone-assisted folding and degradation of misfolded proteins in response to heat.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0009408","count":1},{"id":"GO:0006260","count":1},{"id":"GO:1900035","count":1},{"id":"GO:1901621","count":1},{"id":"GO:0034975","count":1}]},{"hash":"1994183063420759657","title":"Unknown","description":"The top terms show a highly heterogeneous mix of developmental processes across multiple tissues (radial glial scaffolds, endodermal fate, bile duct and endocardial development, enteric nervous system), plus general transcription regulation and mitochondrial DNA packaging. There is no clear, single shared function tying these terms together, so a coherent, specific label cannot be confidently assigned.","confidence":"","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0021943","count":2},{"id":"GO:0060807","count":2},{"id":"GO:0048298","count":2},{"id":"GO:0035622","count":2},{"id":"GO:0060956","count":2}]},{"hash":"1039804508489958707","title":"Mitochondrial fusion and raft-associated signaling","description":"The terms emphasize mitochondrial dynamics (stress-induced fusion, membrane potential regulation) and membrane organization (localization to membrane rafts). Although some immune and neural terms appear, the strongest pattern centers on mitochondria interacting with membrane domains, suggesting a fusion/signaling role tied to membranes.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:1903044","count":3},{"id":"GO:1903905","count":3},{"id":"GO:0001302","count":3},{"id":"GO:0070584","count":3},{"id":"GO:1990046","count":3}]},{"hash":"175514259414267356","title":"ER Stress Response and Protein Quality Control","description":"The cluster is dominated by terms tied to heat-induced stress responses and protein homeostasis: heat response, unfolded protein response, ER protein folding, and ubiquitin-proteasome\u2013mediated quality control, suggesting a functional group focused on managing misfolded proteins during stress. Some terms like DNA replication and translational frameshifting appear as secondary associations, but the core theme centers on ER-associated folding and degradation pathways under heat stress.","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":"DNA replication","top_go_terms":[{"id":"GO:0009408","count":3},{"id":"GO:0006260","count":3},{"id":"GO:1900035","count":3},{"id":"GO:1901621","count":3},{"id":"GO:0034975","count":3}]},{"hash":"399886868570352846","title":"Yeast CVT autophagy and vesicle assembly","description":"These proteins are tied to autophagy-related processes in yeast, notably Cvt vesicle assembly and ribophagy, as well as nucleus\u2013vacuole junction formation, all of which reflect vesicle trafficking and selective turnover in the yeast autophagy pathway. Additional GO terms involving ubiquitin signaling and organelle regulation further support a theme of autophagy-associated vesicle dynamics, though a few other terms appear less directly connected. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0010994","count":2},{"id":"GO:0034517","count":1},{"id":"GO:1904798","count":1},{"id":"GO:0086019","count":1},{"id":"GO:0071255","count":1}]},{"hash":"1522152111242902275","title":"DNA Replication and Repair","description":"The top GO terms cluster around nuclear DNA metabolism, including DNA replication, mitotic replication checkpoint signaling, UV-damage excision repair, and translesion synthesis, with additional terms related to protein complex assembly (homooligomerization/hexamerization). Some terms (peroxisome import, mitochondrial complex III assembly) are outliers, but the dominant theme is DNA replication and DNA damage response.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051260","count":1},{"id":"GO:0016562","count":1},{"id":"GO:0006260","count":1},{"id":"GO:0034214","count":1},{"id":"GO:0034551","count":1}]},{"hash":"837905646957485816","title":"Unknown","description":"The GO terms are diverse and include renal water transport, aging, cell cycle regulation, DNA recombination, corneocyte development, PI dephosphorylation, and xenobiotic response, with several obsolete terms, giving no single cohesive function for this small cluster.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":"DNA recombination","top_go_terms":[{"id":"GO:2001153","count":3},{"id":"GO:0007568","count":3},{"id":"GO:0080111","count":3},{"id":"GO:1900087","count":3},{"id":"GO:0003335","count":3}]},{"hash":"1577384629051931281","title":"Unknown","description":"The top GO terms are highly heterogeneous, spanning cell division, plant ABA signaling, protein assembly, various transport processes in bacteria and plants, DNA replication checkpoints, phosphorylation, and ER-Golgi transport, with no single dominant process. This makes it unclear to assign a coherent, shared function to this small cluster.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0051301","count":2},{"id":"GO:1901527","count":1},{"id":"GO:0034214","count":1},{"id":"GO:0015777","count":1},{"id":"GO:0043213","count":1}]},{"hash":"873841892891532020","title":"Unknown","description":"Top GO terms span very different processes (renal water transport, corneocyte development, DNA recombination, cell-cycle regulation, xenobiotic response) and even include obsolete terms, with no clear shared function tying the proteins together. This appears to be a mixed or noisy cluster rather than a coherent biological theme.","confidence":"","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:2001153","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0080111","count":2},{"id":"GO:1900087","count":2},{"id":"GO:0003335","count":2}]},{"hash":"2259403700573808585","title":"Unknown","description":"The GO terms are diverse (steroid hormone biosynthesis/metabolism, prostaglandin response, bile acid biosynthesis, naphthalene catabolic process, peptide response, vitamin B6 biosynthesis, and stress signaling) with no clear single function tying the proteins together, suggesting no coherent cluster theme.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071799","count":1},{"id":"GO:0001894","count":1},{"id":"GO:0006699","count":1},{"id":"GO:0018931","count":1},{"id":"GO:1901653","count":1}]},{"hash":"1773917215382436973","title":"Protein and polyamine acetylation","description":"The GO terms are dominated by acetylation-related processes: multiple protein acetylation types (N-terminal acetylation, peptidyl-lysine acetylation, histone H4 acetylation) and polyamine acetylation (spermine, putrescine), plus related metabolic steps like N-acetylglucosamine metabolism. This suggests the cluster represents acetylation-centered regulation and metabolism, despite the small size.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0009447","count":1},{"id":"GO:0018003","count":1},{"id":"GO:2000025","count":1},{"id":"GO:0006044","count":1},{"id":"GO:0032919","count":1}]},{"hash":"2034885539414823898","title":"Vitamin cofactor metabolism","description":"This cluster is mainly driven by metabolic processes involving vitamins and cofactors (thiamine biosynthesis, tetrahydrofolate metabolism, and dihydrolipoamide metabolism), suggesting a cohesive theme of vitamin/cofactor\u2013related pathways. A few other terms (xenobiotic/nutrient response and occasional development terms) are present but appear less central to the core theme.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042493","count":2},{"id":"GO:0007584","count":2},{"id":"GO:0046886","count":1},{"id":"GO:0045648","count":1},{"id":"GO:0009228","count":1}]},{"hash":"1300714483003049193","title":"Chloroplast Biogenesis and Light Response","description":"These terms cluster around chloroplast biology and light responses in plants: positive regulation of protein import into chloroplast stroma, chloroplast organization, and de-etiolation all point to chloroplast development and light-mediated changes. The other terms (vacuolar protein processing, cobalamin biosynthesis) are less connected, so the label emphasizes chloroplast biogenesis and light response as the dominant theme.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1904216","count":1},{"id":"GO:0009704","count":1},{"id":"GO:0009658","count":1},{"id":"GO:0006624","count":1},{"id":"GO:0009236","count":1}]},{"hash":"1151942617008418405","title":"Amino Acid Catabolism and Mitochondrial Metabolism","description":"The prominent GO terms point to catabolic processing of amino acids (alanine, valine) alongside cofactor-related metabolism (thiamine biosynthesis, tetrahydrofolate metabolism) and mitochondrial energy production (NADH to ubiquinone). These together suggest a metabolic/energy-production focus, with a few outlier terms related to development or neurotransmitter regulation that are less central to the cluster\u2019s core theme. ","confidence":"Medium","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0042853","count":3},{"id":"GO:0009228","count":2},{"id":"GO:0046653","count":2},{"id":"GO:0010725","count":2},{"id":"GO:0014063","count":2}]},{"hash":"2298127855140376985","title":"Acetyl-CoA\u2013driven central carbon metabolism and lipid biosynthesis","description":"These proteins show a coherent signal for central carbon metabolism, with glycolysis and pyruvate decarboxylation feeding into acetyl-CoA, which then fuels the TCA cycle, gluconeogenesis, and lipid biosynthesis (malonyl-CoA and long-chain fatty acids). Amino-acid catabolism of leucine and lysine also contributes acetyl-CoA, supporting energy production and lipid synthesis. Some terms like sodium transport and pyrimidine metabolism are peripheral, but the core theme is acetyl-CoA\u2013centered metabolism.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0033512","count":3},{"id":"GO:2001295","count":3},{"id":"GO:0006099","count":3},{"id":"GO:0006814","count":3},{"id":"GO:0006096","count":3}]},{"hash":"923969804899397532","title":"Ribosome Biogenesis and Translation","description":"The cluster is dominated by ribosome-related processes: ribosome biogenesis, export of the large subunit, cytoplasmic translation, and tRNA modification. While there are some cell-cycle and cell-division terms present, the strongest and most frequent terms point to ribosome assembly and protein synthesis as the core function of this group.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":2},{"id":"GO:0000055","count":2},{"id":"GO:0002181","count":2},{"id":"GO:1903833","count":2},{"id":"GO:1901001","count":2}]},{"hash":"2247625450435092061","title":"Membrane Transport","description":"This cluster is characterized by GO terms centered on transport across membranes and substrates being moved (xenobiotics, daunorubicin, taurine, long-chain fatty acids into peroxisomes, bacteriocins, and oligopeptides). The preponderance of transport-related terms supports naming the group as membrane transporters or transport-associated proteins, with nucleotide-excision repair appearing as a potential outlier. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0046618","count":1},{"id":"GO:0006289","count":1},{"id":"GO:0015910","count":1},{"id":"GO:0015777","count":1},{"id":"GO:0043213","count":1}]},{"hash":"1370901042910492937","title":"TCA and acetyl-CoA metabolism","description":"This cluster is dominated by GO terms for acetyl-CoA biosynthesis, the TCA cycle, succinyl-CoA metabolism, and biotin biosynthesis, all pointing to central carbon metabolism and energy production. Redox state response is present, and there are a few transcription-related terms, but the core signal is metabolic processing of acetyl-CoA and TCA intermediates.","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0006085","count":2},{"id":"GO:0006099","count":2},{"id":"GO:0045892","count":2},{"id":"GO:0006104","count":2},{"id":"GO:0051775","count":2}]},{"hash":"1751311446475629936","title":"Cofactor and vitamin biosynthesis","description":"This cluster is driven by GO terms for the biosynthesis of multiple cofactors and vitamins (biotin, thiamine, lipoate, molybdopterin, PQQ, and heme precursor protoporphyrinogen IX), indicating a common theme of cofactor assembly. While a couple of terms touch broader metabolism (tRNA methylation, choline catabolism), the dominant signal is cofactor production pathways.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006782","count":1},{"id":"GO:0030488","count":1},{"id":"GO:0042426","count":1},{"id":"GO:0018339","count":1},{"id":"GO:0009107","count":1}]},{"hash":"918937408310988751","title":"Unknown","description":"The top GO terms span diverse processes (nematode development, metabolism, mRNA capping, xenobiotic response) with no clear shared function among the three proteins, and there are no edges linking them. This makes it impossible to assign a specific, representative label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0018996","count":1},{"id":"GO:0010269","count":1},{"id":"GO:0043050","count":1},{"id":"GO:0035264","count":1},{"id":"GO:0035934","count":1}]},{"hash":"1868685760057203410","title":"Mitotic Cohesion and Ribosome Biogenesis","description":"The cluster shows strong signals for mitotic sister chromatid cohesion and its establishment, plus ribosome biogenesis and translation, suggesting proteins involved in nuclear processes linking cell division with ribosome production. Some RNA polymerase import terms are obsolete and may reflect annotation noise, but the core theme centers on mitosis-related cohesion and ribosome biogenesis.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0007064","count":2},{"id":"GO:0044376","count":2},{"id":"GO:1990022","count":2},{"id":"GO:0034087","count":2},{"id":"GO:0006576","count":2}]},{"hash":"1372116717641210843","title":"T cell and hematopoietic differentiation","description":"The dominant GO terms point to immune cell development, especially T cell differentiation in the thymus and granulocyte differentiation, along with hematopoietic stem cell proliferation, indicating a cluster focused on immune lineage formation. A number of metabolic terms are present but appear ancillary rather than defining. Confidence is High.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0030851","count":1},{"id":"GO:0033077","count":1},{"id":"GO:1903955","count":1},{"id":"GO:0046638","count":1},{"id":"GO:0071425","count":1}]},{"hash":"1405953430175499521","title":"Fungal Cell Wall Remodeling and Biofilm Formation","description":"The GO terms cluster around fungal-specific cell wall remodeling (beta-glucan metabolism, disassembly) and lipid glycoside catabolism (ergosteryl glucoside), together with catabolic processes for plant polysaccharides (cellulose, xylan, mannan) and biofilm formation on host or inanimate substrates, pointing to a fungal metabolism facilitating cell wall dynamics and biofilm lifestyle.","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0030245","count":1},{"id":"GO:0044407","count":1},{"id":"GO:0046355","count":1},{"id":"GO:1904541","count":1},{"id":"GO:0044011","count":1}]},{"hash":"1214995245126657842","title":"Unknown","description":"The GO terms are highly heterogeneous, spanning metabolism (CoA biosynthesis, glucose response), post-translational modification (phosphorylation), transcription regulation, cell proliferation, neuronal signaling, and even obsolete annotations. With no clear shared function or pathway across the proteins, a cohesive label cannot be reliably assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":1},{"id":"GO:0015937","count":1},{"id":"GO:0051260","count":1},{"id":"GO:1904797","count":1},{"id":"GO:0051968","count":1}]},{"hash":"1786037916067874245","title":"Unknown","description":"The GO terms present are a scattered mix of metabolism (thiamine biosynthesis, mitochondrial electron transport), hematopoietic differentiation (erythrocyte and megakaryocyte), neurotransmitter regulation (serotonin secretion), and immune defense, with several obsolete terms. There is no clear, cohesive function binding these proteins, especially given zero edges/triangles, so a single representative label cannot be confidently assigned.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009228","count":2},{"id":"GO:0010725","count":2},{"id":"GO:0014063","count":2},{"id":"GO:0043046","count":2},{"id":"GO:0042742","count":2}]},{"hash":"532293335402751315","title":"Peroxisomal glyoxylate and fatty acid metabolism","description":"The top GO terms point to peroxisomal pathways handling short-chain metabolite oxidation and processing, including fatty acid alpha-oxidation, glycolate catabolism, and photorespiration, which are all peroxisome-associated. While some terms are obsolete or peripheral (e.g., mandelate metabolism, isoprenoid biosynthesis, or stress responses), the core signal is peroxisomal carbon metabolism connecting glyoxylate/glycolate processing and fatty acid turnover. This supports a cohesive theme of peroxisomal metabolic flux rather than a single isolated pathway.","confidence":"High","size":3,"edges":1,"triangles":0,"max_degree":1,"top_function":null,"top_go_terms":[{"id":"GO:0055114","count":2},{"id":"GO:0018924","count":1},{"id":"GO:0008299","count":1},{"id":"GO:0019516","count":1},{"id":"GO:0001561","count":1}]},{"hash":"515095155306967815","title":"Mitochondrial energy metabolism and cofactors","description":"Top GO terms point to a mitochondria-centric metabolic module: NADH to ubiquinone electron transport, dihydrolipoamide/lipoate metabolism, and thiamine biosynthesis linked to key cofactors, along with redox homeostasis and membrane potential regulation. Some terms (aging, gastrulation, camphor catabolic process) appear noisy or obsolete, but the core signal supports a mitochondrial energy/metabolic cluster.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0045454","count":3},{"id":"GO:0009228","count":2},{"id":"GO:0007568","count":2},{"id":"GO:0019383","count":2},{"id":"GO:0051068","count":2}]},{"hash":"1488185016422685969","title":"Mitotic spindle organization and cytokinesis","description":"The top GO terms cluster around cytoplasmic microtubule organization, spindle assembly/duplication, spindle midzone formation, and cytokinesis, indicating proteins involved in mitotic machinery and cell division. While there are a couple of terms related to neuron differentiation and immune signaling, their support is minimal compared to the microtubule/cytokinesis signals. Overall, the dominant theme is microtubule-based division processes such as spindle formation and cytokinesis, which justifies the label. ","confidence":"High","size":3,"edges":3,"triangles":1,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0031122","count":2},{"id":"GO:0030182","count":2},{"id":"GO:1903087","count":2},{"id":"GO:0071353","count":2},{"id":"GO:0051256","count":2}]},{"hash":"2167740224782509494","title":"ATP synthase subunits","description":"This cluster is labeled by the GO term proton motive force-driven ATP synthesis, suggesting components of the ATP synthase complex that harness the proton gradient to produce ATP. Given only a single specific term and no interactions described, confidence is moderate but not strong.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0015986","count":1}]},{"hash":"665384698156912389","title":"Unknown","description":"The GO terms are diverse (lipoprotein biosynthesis, redox, ER stress, NK cell cytotoxicity, viral process, NF-kappaB signaling, etc.) with several obsolete entries, and there isn\u2019t a single clear function or pathway uniting the proteins in this cluster. The mix suggests no cohesive theme rather than a defined biological process.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042158","count":2},{"id":"GO:0055114","count":2},{"id":"GO:0033158","count":1},{"id":"GO:0034976","count":1},{"id":"GO:0042267","count":1}]},{"hash":"33064699787475538","title":"RNA processing and ribosome biogenesis","description":"The top GO terms cluster around RNA processing (miRNA catabolic process, pre-miRNA processing, CRD-mediated mRNA stabilization) and ribosome biogenesis (ribosome biogenesis, nucleolar large rRNA transcription by RNA polymerase I), with related transcriptional regulation terms (DNA-templated transcription, transcription antitermination). This suggests a nuclear RNA metabolism and ribosome assembly theme for the cluster; a few unrelated stress-related terms appear but do not dominate. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1902219","count":1},{"id":"GO:0010587","count":1},{"id":"GO:0031054","count":1},{"id":"GO:0031564","count":1},{"id":"GO:1901724","count":1}]},{"hash":"1340464005628060067","title":"Unknown","description":"The listed GO terms cover cholesterol biosynthesis, fatty acid oxidation, sodium transport, prostaglandin/IL-6 signaling, hydrogen sulfide biosynthesis, and guanylate cyclase activity, indicating metabolism, transport, and signaling functions with no evident common biological process. The lack of edges and a cohesive theme suggests no single function characterizes this cluster.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0006695","count":1},{"id":"GO:0010124","count":1},{"id":"GO:0032770","count":1},{"id":"GO:0006814","count":1},{"id":"GO:1901206","count":1}]},{"hash":"1187714953295321735","title":"Glycolysis and Fructose Metabolism","description":"The GO terms are dominated by carbohydrate metabolism, glycolysis, and fructose pathways, with related steps like carbohydrate phosphorylation and pentose-phosphate shunt regulation, pointing to a shared role in central carbon metabolism.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0071555","count":1},{"id":"GO:0005975","count":1},{"id":"GO:0006000","count":1},{"id":"GO:0046835","count":1},{"id":"GO:0043456","count":1}]},{"hash":"1992997647319324374","title":"Ribosome biogenesis and translational fidelity","description":"The top GO terms are dominated by ribosome biogenesis, rRNA modification (pseudouridine synthesis), translation, and processes maintaining or regulating accurate translation (fidelity and initiation). Several terms about transcription termination/antitermination appear but likely reflect RNA-processing/translation coupling rather than a core separate function; overall the cluster appears centered on ribosome assembly and ensuring proper translation, with some stress/antibiotic response signals. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042254","count":1},{"id":"GO:0045903","count":1},{"id":"GO:0000455","count":1},{"id":"GO:0034605","count":1},{"id":"GO:0006353","count":1}]},{"hash":"1776805723700367905","title":"Calcium and cGMP signaling in heart and brain","description":"The top GO terms mix cardiovascular development (blood vessel branching, heart development) with neural plasticity (long-term synaptic potentiation) and calcium signaling (calcium release into cytosol) plus guanylate cyclase activity (cGMP signaling). This points to a common theme of calcium- and cGMP-dependent signaling pathways operating in both heart/vessel development and brain synaptic function. Some terms are broader or obsolete, but the core theme remains signaling dynamics linked to calcium and cGMP in cardiovascular and nervous system contexts.","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0001569","count":1},{"id":"GO:1901841","count":1},{"id":"GO:1900271","count":1},{"id":"GO:0060291","count":1},{"id":"GO:0090151","count":1}]},{"hash":"175715843939457608","title":"Unknown","description":"The set of GO terms is highly diverse, including circadian rhythm regulation, ubiquitin-dependent protein degradation, ergosterol biosynthesis, nitrate assimilation, arsenic response, oxidative stress-induced apoptotic signaling, and cell-cycle checkpoints. There is no single unifying function strong enough to define the cluster, so 'Unknown' is the most honest label.","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0042752","count":1},{"id":"GO:0031146","count":1},{"id":"GO:0032443","count":1},{"id":"GO:0000083","count":1},{"id":"GO:1902916","count":1}]},{"hash":"602268917997313733","title":"MVB-mediated endosome-to-vacuole trafficking","description":"GO:0032511 points to transport from late endosome to vacuole via multivesicular body sorting, i.e., MVB/ESCRT endosomal trafficking. The cluster likely comprises proteins involved in this endosomal sorting pathway, but with only one annotation and no network edges, the support is modest. ","confidence":"Medium","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0032511","count":1}]},{"hash":"1773630752075736381","title":"TLR Signaling and Interferon Production","description":"The enrichment includes Toll-like receptor signaling (TLR8/9) and regulation of interferon production, dendritic cell cytokine regulation, and fungal response, pointing to innate immune sensing and IFN-mediated responses. Some unrelated terms (floral meristem, bone remodeling) appear but overall the cluster centers on TLR-driven antiviral/antifungal signaling and cytokine amplification.","confidence":"High","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:0009620","count":1},{"id":"GO:0045359","count":1},{"id":"GO:0034162","count":1},{"id":"GO:0010080","count":1},{"id":"GO:1900155","count":1}]},{"hash":"1960946723018229171","title":"Unknown","description":"Unknown","confidence":"","size":3,"edges":0,"triangles":0,"max_degree":0,"top_function":null,"top_go_terms":[{"id":"GO:1901006","count":1},{"id":"GO:0055114","count":1},{"id":"GO:0080110","count":1},{"id":"GO:0042351","count":1},{"id":"GO:0009103","count":1}]},{"hash":"826789591641937790","title":"Amino acid biosynthesis and salvage","description":"The top GO terms center on amino acid metabolism, notably L-threonine biosynthesis and methionine salvage, suggesting a focus on amino acid biosynthesis and recycling. Phosphorylation and proteolysis hint at regulatory control of these pathways, supporting a label that emphasizes amino acid metabolism and its regulation. ","confidence":"Medium","size":3,"edges":2,"triangles":0,"max_degree":2,"top_function":null,"top_go_terms":[{"id":"GO:0016310","count":2},{"id":"GO:0019509","count":2},{"id":"GO:0009088","count":2},{"id":"GO:0019284","count":2},{"id":"GO:0046677","count":2}]}]